fix(terminal): use ctrl shift c for output copy

Capture Ctrl+Shift+C before xterm input handling and copy selected output through a browser-compatible fallback. Preserve Ctrl+C as terminal input.

.atl/.skill-registry.cache.json

@@ -0,0 +1,3 @@
+{
+  "fingerprint": "e7b3130f52a328d4051e75364e5394ac63df60c6"
+}

.atl/skill-registry.md

@@ -0,0 +1,33 @@
+# Skill Registry — headquarter
+
+<!-- Auto-generated by gentle-pi extensions/skill-registry.ts. Run /skill-registry:refresh to regenerate. -->
+
+Last updated: 2026-06-17
+
+## Sources scanned
+
+- .opencode/skills
+- .claude/skills
+
+## Contract
+
+**Delegator use only.** This registry is an index, not a summary. Any agent that launches subagents reads it to select relevant skills, then passes exact `SKILL.md` paths for the subagent to read before work.
+
+`SKILL.md` remains the source of truth. Do not inject generated summaries or compact rules by default; pass paths so subagents load the full runtime contract and preserve author intent.
+
+## Skills
+
+| Skill | Trigger / description | Scope | Path |
+| --- | --- | --- | --- |
+| `openspec-apply-change` | Implement tasks from an OpenSpec change. Use when the user wants to start implementing, continue implementation, or work through tasks. | project | `/home/user/headquarter/.opencode/skills/openspec-apply-change/SKILL.md` |
+| `openspec-archive-change` | Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete. | project | `/home/user/headquarter/.opencode/skills/openspec-archive-change/SKILL.md` |
+| `openspec-explore` | Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change. | project | `/home/user/headquarter/.opencode/skills/openspec-explore/SKILL.md` |
+| `openspec-propose` | Propose a new change with all artifacts generated in one step. Use when the user wants to quickly describe what they want to build and get a complete proposal with design, specs, and tasks ready for implementation. | project | `/home/user/headquarter/.opencode/skills/openspec-propose/SKILL.md` |
+| `sift-backlog` | Triage and organize backlog tasks into actionable plans. Use when asked to review the backlog, prioritize tasks, create plans from backlog items, or move tasks from backlog to open status. Handles the full workflow of listing backlog tasks, grouping related tasks into plans, setting priorities and dependencies, activating plans, and changing task status from backlog to open. | project | `/home/user/headquarter/.claude/skills/sift-backlog/SKILL.md` |
+
+## Loading protocol
+
+1. Match task context and target files against the `Trigger / description` column.
+2. Pass only the matching `Path` values to the subagent under `## Skills to load before work`.
+3. Instruct the subagent to read those exact `SKILL.md` files before reading, writing, reviewing, testing, or creating artifacts.
+4. If no matching skill exists, proceed without project skill injection and report `skill_resolution: none`.

.claude/.pi-map.index.md

@@ -0,0 +1,20 @@
+# .claude (index)
+dir: .claude
+
+## role
+Configuration directory for Claude AI assistant settings and custom instructions.
+## parent
+index: ./.pi-map.index.md
+map: ./.pi-map.md
+## children
+- .claude/skills
+  index: .claude/skills/.pi-map.index.md
+  map: .claude/skills/.pi-map.md
+## files
+## links
+index: .claude/.pi-map.index.md
+map: .claude/.pi-map.md
+## workflows
+-
+## dirty
+-

.claude/.pi-map.md

@@ -0,0 +1,18 @@
+# .claude
+dir: .claude
+
+index: .claude/.pi-map.index.md
+
+## role
+Configuration directory for Claude AI assistant settings and custom instructions.
+## files
+## arch
+Simple flat-file configuration storage with no executable code, using human-readable text files for AI behavior customization.
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-

.claude/skills/.pi-map.index.md

@@ -0,0 +1,20 @@
+# .claude/skills (index)
+dir: .claude/skills
+
+## role
+Contains skill definitions and configuration files for the Claude AI assistant to extend its capabilities with specialized behaviors and domain-specific expertise.
+## parent
+index: .claude/.pi-map.index.md
+map: .claude/.pi-map.md
+## children
+- .claude/skills/sift-backlog
+  index: .claude/skills/sift-backlog/.pi-map.index.md
+  map: .claude/skills/sift-backlog/.pi-map.md
+## files
+## links
+index: .claude/skills/.pi-map.index.md
+map: .claude/skills/.pi-map.md
+## workflows
+-
+## dirty
+-

.claude/skills/.pi-map.md

@@ -0,0 +1,18 @@
+# .claude/skills
+dir: .claude/skills
+
+index: .claude/skills/.pi-map.index.md
+
+## role
+Contains skill definitions and configuration files for the Claude AI assistant to extend its capabilities with specialized behaviors and domain-specific expertise.
+## files
+## arch
+Declarative skill configuration system using structured metadata files (likely YAML/JSON) that define prompts, tools, and context boundaries for modular AI capability extensions.
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-

.claude/skills/sift-backlog/.pi-map.index.md

@@ -0,0 +1,19 @@
+# .claude/skills/sift-backlog (index)
+dir: .claude/skills/sift-backlog
+
+## role
+Provides a workflow skill for triaging, organizing, and activating backlog tasks into actionable plans using a custom CLI tool.
+## parent
+index: .claude/skills/.pi-map.index.md
+map: .claude/skills/.pi-map.md
+## children
+-
+## files
+- SKILL.md
+## links
+index: .claude/skills/sift-backlog/.pi-map.index.md
+map: .claude/skills/sift-backlog/.pi-map.md
+## workflows
+-
+## dirty
+-

.claude/skills/sift-backlog/.pi-map.md

@@ -0,0 +1,19 @@
+# .claude/skills/sift-backlog
+dir: .claude/skills/sift-backlog
+
+index: .claude/skills/sift-backlog/.pi-map.index.md
+
+## role
+Provides a workflow skill for triaging, organizing, and activating backlog tasks into actionable plans using a custom CLI tool.
+## files
+- SKILL.md | Defines a workflow skill for triaging, organizing, and activating backlog tasks into actionable plans using a custom CLI tool. | dep: sf CLI (task, plan, dependency, update subcommands)
+## arch
+Skill-based workflow automation using markdown-defined CLI tooling and structured task management patterns.
+## tags
+skill, defines, workflow, triaging, organizing, activating, backlog, tasks
+## symbols
+-
+## workflows
+-
+## dirty
+-

.gitignore

@@ -17,6 +17,7 @@ __pycache__/
 *.so
 .python-version
 .venv/
+.venv-test/
 venv/
 env/
 .pytest_cache/
@@ -49,5 +50,11 @@ apps/web/dist/
 .DS_Store
 Thumbs.db
 /.stoneforge/.worktrees/
-# Local Pi runtime state
+# Pi / agent cache
+.pi/
 .atl/
+.sisyphus/
+.pi-lens/
+minerv3/
+.cache/
+openspec-audit-report.md

.opencode/.pi-map.index.md

@@ -0,0 +1,23 @@
+# .opencode (index)
+dir: .opencode
+
+## role
+This appears to be a configuration or metadata directory for the OpenCode AI coding assistant tool.
+## parent
+index: ./.pi-map.index.md
+map: ./.pi-map.md
+## children
+- .opencode/commands
+  index: .opencode/commands/.pi-map.index.md
+  map: .opencode/commands/.pi-map.md
+- .opencode/skills
+  index: .opencode/skills/.pi-map.index.md
+  map: .opencode/skills/.pi-map.md
+## files
+## links
+index: .opencode/.pi-map.index.md
+map: .opencode/.pi-map.md
+## workflows
+-
+## dirty
+-

.opencode/.pi-map.md

@@ -0,0 +1,18 @@
+# .opencode
+dir: .opencode
+
+index: .opencode/.pi-map.index.md
+
+## role
+This appears to be a configuration or metadata directory for the OpenCode AI coding assistant tool.
+## files
+## arch
+Hidden directory storing tool-specific state; no discernible software architecture as it contains no source files.
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-

.opencode/commands/.pi-map.index.md

@@ -0,0 +1,22 @@
+# .opencode/commands (index)
+dir: .opencode/commands
+
+## role
+Defines AI assistant command workflows for an OpenSpec-based development system, covering task execution, change archival, exploratory analysis, and new change proposal generation.
+## parent
+index: .opencode/.pi-map.index.md
+map: .opencode/.pi-map.md
+## children
+-
+## files
+- opsx-apply.md
+- opsx-archive.md
+- opsx-explore.md
+- opsx-propose.md
+## links
+index: .opencode/commands/.pi-map.index.md
+map: .opencode/commands/.pi-map.md
+## workflows
+-
+## dirty
+-

.opencode/commands/.pi-map.md

@@ -0,0 +1,22 @@
+# .opencode/commands
+dir: .opencode/commands
+
+index: .opencode/commands/.pi-map.index.md
+
+## role
+Defines AI assistant command workflows for an OpenSpec-based development system, covering task execution, change archival, exploratory analysis, and new change proposal generation.
+## files
+- opsx-apply.md | Implement tasks from an OpenSpec change by selecting a change, reading context files, and executing pending tasks in a loop until completion or blocked. | dep: openspec CLI, AskUserQuestion tool, filesystem access
+- opsx-archive.md | Defines a workflow for archiving completed changes in an experimental openspec-based development system, including validation, spec sync assessment, and user confirmation steps. | dep: openspec CLI, AskUserQuestion tool, Task tool, Skill tool, filesystem operations
+- opsx-explore.md | Defines the "explore mode" stance and guidelines for an AI assistant to think through ideas, investigate problems, and clarify requirements without implementing code. | dep: OpenSpec system, ASCII diagrams, codebase investigation tools
+- opsx-propose.md | Defines an AI assistant workflow for proposing new changes by creating a scaffolded change directory and generating all required artifacts (proposal.md, design.md, tasks.md) in dependency order using the openspec CLI tool. | dep: openspec CLI, AskUserQuestion tool, TodoWrite tool
+## arch
+Markdown-based command specifications using a structured workflow pattern with sequential steps, file I/O operations, CLI tool integration (openspec), and human-in-the-loop decision points for validation and confirmation.
+## tags
+opsx, tasks, openspec, change, openspec cli, askuserquestion tool, defines, explore
+## symbols
+-
+## workflows
+-
+## dirty
+-

.opencode/skills/.pi-map.index.md

@@ -0,0 +1,29 @@
+# .opencode/skills (index)
+dir: .opencode/skills
+
+## role
+Contains custom AI agent skills or capabilities that extend the base functionality of the OpenCode framework with specialized tools and behaviors.
+## parent
+index: .opencode/.pi-map.index.md
+map: .opencode/.pi-map.md
+## children
+- .opencode/skills/openspec-apply-change
+  index: .opencode/skills/openspec-apply-change/.pi-map.index.md
+  map: .opencode/skills/openspec-apply-change/.pi-map.md
+- .opencode/skills/openspec-archive-change
+  index: .opencode/skills/openspec-archive-change/.pi-map.index.md
+  map: .opencode/skills/openspec-archive-change/.pi-map.md
+- .opencode/skills/openspec-explore
+  index: .opencode/skills/openspec-explore/.pi-map.index.md
+  map: .opencode/skills/openspec-explore/.pi-map.md
+- .opencode/skills/openspec-propose
+  index: .opencode/skills/openspec-propose/.pi-map.index.md
+  map: .opencode/skills/openspec-propose/.pi-map.md
+## files
+## links
+index: .opencode/skills/.pi-map.index.md
+map: .opencode/skills/.pi-map.md
+## workflows
+-
+## dirty
+-

.opencode/skills/.pi-map.md

@@ -0,0 +1,18 @@
+# .opencode/skills
+dir: .opencode/skills
+
+index: .opencode/skills/.pi-map.index.md
+
+## role
+Contains custom AI agent skills or capabilities that extend the base functionality of the OpenCode framework with specialized tools and behaviors.
+## files
+## arch
+Modular skill plugin architecture where individual capabilities are registered as discrete, composable units that can be dynamically loaded and invoked by the agent system.
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-

.opencode/skills/openspec-apply-change/.pi-map.index.md

@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-apply-change (index)
+dir: .opencode/skills/openspec-apply-change
+
+## role
+Provides an AI assistant skill that automates implementation of OpenSpec specification changes through a structured, CLI-driven workflow.
+## parent
+index: .opencode/skills/.pi-map.index.md
+map: .opencode/skills/.pi-map.md
+## children
+-
+## files
+- SKILL.md
+## links
+index: .opencode/skills/openspec-apply-change/.pi-map.index.md
+map: .opencode/skills/openspec-apply-change/.pi-map.md
+## workflows
+-
+## dirty
+-

.opencode/skills/openspec-apply-change/.pi-map.md

@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-apply-change
+dir: .opencode/skills/openspec-apply-change
+
+index: .opencode/skills/openspec-apply-change/.pi-map.index.md
+
+## role
+Provides an AI assistant skill that automates implementation of OpenSpec specification changes through a structured, CLI-driven workflow.
+## files
+- SKILL.md | Defines an AI assistant skill for implementing tasks from an OpenSpec change using a spec-driven workflow with the openspec CLI. | dep: openspec CLI, AskUserQuestion tool, filesystem access
+## arch
+Skill-based plugin architecture using markdown-defined capabilities with structured workflow steps (analyze, plan, implement, verify) and external CLI tool integration.
+## tags
+skill, openspec, defines, assistant, implementing, tasks, change, spec
+## symbols
+-
+## workflows
+-
+## dirty
+-

.opencode/skills/openspec-archive-change/.pi-map.index.md

@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-archive-change (index)
+dir: .opencode/skills/openspec-archive-change
+
+## role
+Defines an automation skill for archiving completed changes in an experimental workflow using the openspec CLI.
+## parent
+index: .opencode/skills/.pi-map.index.md
+map: .opencode/skills/.pi-map.md
+## children
+-
+## files
+- SKILL.md
+## links
+index: .opencode/skills/openspec-archive-change/.pi-map.index.md
+map: .opencode/skills/openspec-archive-change/.pi-map.md
+## workflows
+-
+## dirty
+-

.opencode/skills/openspec-archive-change/.pi-map.md

@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-archive-change
+dir: .opencode/skills/openspec-archive-change
+
+index: .opencode/skills/openspec-archive-change/.pi-map.index.md
+
+## role
+Defines an automation skill for archiving completed changes in an experimental workflow using the openspec CLI.
+## files
+- SKILL.md | Defines a skill for archiving completed changes in an experimental workflow using the openspec CLI. | dep: openspec CLI, AskUserQuestion tool, Task tool, Skill tool, openspec-sync-specs skill
+## arch
+Skill-based plugin architecture following a declarative markdown skill definition pattern for CLI workflow automation.
+## tags
+skill, openspec, defines, archiving, completed, changes, experimental, workflow
+## symbols
+-
+## workflows
+-
+## dirty
+-

.opencode/skills/openspec-explore/.pi-map.index.md

@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-explore (index)
+dir: .opencode/skills/openspec-explore
+
+## role
+Provides a conversational exploration skill for OpenSpec CLI that enables non-implementation ideation, problem investigation, and requirements clarification.
+## parent
+index: .opencode/skills/.pi-map.index.md
+map: .opencode/skills/.pi-map.md
+## children
+-
+## files
+- SKILL.md
+## links
+index: .opencode/skills/openspec-explore/.pi-map.index.md
+map: .opencode/skills/openspec-explore/.pi-map.md
+## workflows
+-
+## dirty
+-

.opencode/skills/openspec-explore/.pi-map.md

@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-explore
+dir: .opencode/skills/openspec-explore
+
+index: .opencode/skills/openspec-explore/.pi-map.index.md
+
+## role
+Provides a conversational exploration skill for OpenSpec CLI that enables non-implementation ideation, problem investigation, and requirements clarification.
+## files
+- SKILL.md | Defines a conversational "explore mode" skill for OpenSpec CLI that acts as a thinking partner for exploring ideas, investigating problems, and clarifying requirements without implementing code. | dep: openspec CLI
+## arch
+Skill-based plugin architecture using markdown-defined behavioral specifications with conversational AI patterns, separating exploration/thinking workflows from implementation tasks.
+## tags
+skill, defines, conversational, explore, mode, openspec, cli, acts
+## symbols
+-
+## workflows
+-
+## dirty
+-

.opencode/skills/openspec-propose/.pi-map.index.md

@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-propose (index)
+dir: .opencode/skills/openspec-propose
+
+## role
+Automates the creation of structured software change proposals through a scaffolded directory workflow using the openspec CLI.
+## parent
+index: .opencode/skills/.pi-map.index.md
+map: .opencode/skills/.pi-map.md
+## children
+-
+## files
+- SKILL.md
+## links
+index: .opencode/skills/openspec-propose/.pi-map.index.md
+map: .opencode/skills/openspec-propose/.pi-map.md
+## workflows
+-
+## dirty
+-

.opencode/skills/openspec-propose/.pi-map.md

@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-propose
+dir: .opencode/skills/openspec-propose
+
+index: .opencode/skills/openspec-propose/.pi-map.index.md
+
+## role
+Automates the creation of structured software change proposals through a scaffolded directory workflow using the openspec CLI.
+## files
+- SKILL.md | Defines an AI skill that automates proposing new software changes by scaffolding a directory structure and generating dependent artifacts (proposal, design, tasks) using the openspec CLI workflow. | dep: openspec CLI, AskUserQuestion tool, TodoWrite tool
+## arch
+Template-driven skill architecture following a sequential artifact generation pattern (proposal → design → tasks) with CLI-based workflow automation.
+## tags
+skill, defines, automates, proposing, new, software, changes, scaffolding
+## symbols
+-
+## workflows
+-
+## dirty
+-

.pi-map.index.md

@@ -0,0 +1,82 @@
+# . (index)
+dir: .
+
+## Project Map Protocol
+
+1. Read this protocol and the root `.pi-map.index.md` first.
+2. Use `index:` / `map:` references to open relevant directory indexes and maps.
+3. Load indexes before rich maps during task-start navigation.
+4. Read the local rich map and actual source before editing.
+5. Treat non-empty `## dirty` sections in either artifact as stale.
+6. If source and generated artifacts disagree, trust source.
+7. If map and index disagree, trust neither blindly; verify from source and regenerate the pair.
+8. After editing source, run `project_map_patch` for each changed file.
+9. Before broad architectural claims or final handoff, run `project_map_validate` when freshness matters.
+
+Trust boundary: index routes, map orients, source decides.
+
+## role
+Package .
+## parent
+-
+## children
+- .atl
+  index: .atl/.pi-map.index.md
+  map: .atl/.pi-map.md
+- .claude
+  index: .claude/.pi-map.index.md
+  map: .claude/.pi-map.md
+- .opencode
+  index: .opencode/.pi-map.index.md
+  map: .opencode/.pi-map.md
+- .pi
+  index: .pi/.pi-map.index.md
+  map: .pi/.pi-map.md
+- .sisyphus
+  index: .sisyphus/.pi-map.index.md
+  map: .sisyphus/.pi-map.md
+- .stoneforge
+  index: .stoneforge/.pi-map.index.md
+  map: .stoneforge/.pi-map.md
+- apps
+  index: apps/.pi-map.index.md
+  map: apps/.pi-map.md
+- docs
+  index: docs/.pi-map.index.md
+  map: docs/.pi-map.md
+- e2e
+  index: e2e/.pi-map.index.md
+  map: e2e/.pi-map.md
+- openspec
+  index: openspec/.pi-map.index.md
+  map: openspec/.pi-map.md
+- scripts
+  index: scripts/.pi-map.index.md
+  map: scripts/.pi-map.md
+- tool-images
+  index: tool-images/.pi-map.index.md
+  map: tool-images/.pi-map.md
+- uploads
+  index: uploads/.pi-map.index.md
+  map: uploads/.pi-map.md
+## files
+- .env.example
+- .gitignore
+- AGENTS.md
+- CHANGELOG.md
+- Makefile
+- README.md
+- docker-compose.traefik.yml
+- docker-compose.yml
+- progress.md
+- swap-pane
+- ui-audit-spacing-typography.md
+- ui-rework-foundations-apply.md
+- ui-rework-pass2-apply.md
+## links
+index: ./.pi-map.index.md
+map: ./.pi-map.md
+## workflows
+-
+## dirty
+-

.pi-map.md

@@ -0,0 +1,45 @@
+# .
+dir: .
+
+index: ./.pi-map.index.md
+
+## Project Map Protocol
+
+1. Read this protocol and the root `.pi-map.index.md` first.
+2. Use `index:` / `map:` references to open relevant directory indexes and maps.
+3. Load indexes before rich maps during task-start navigation.
+4. Read the local rich map and actual source before editing.
+5. Treat non-empty `## dirty` sections in either artifact as stale.
+6. If source and generated artifacts disagree, trust source.
+7. If map and index disagree, trust neither blindly; verify from source and regenerate the pair.
+8. After editing source, run `project_map_patch` for each changed file.
+9. Before broad architectural claims or final handoff, run `project_map_validate` when freshness matters.
+
+Trust boundary: index routes, map orients, source decides.
+
+## role
+Package .
+## files
+- .env.example | Provides example environment variable configuration for a full-stack application with database, caching, authentication, and deployment settings
+- .gitignore | Specifies files and directories for Git to ignore across a project using Beads/Dolt, Python, Node, and various IDE/OS tooling. | dep: git, dolt, beads, python, node, npm, yarn, pnpm, pytest, mypy, ruff, coverage
+- AGENTS.md | Defines operational guidelines and workflows for AI agents collaborating on a software project governed by OpenSpec | dep: OpenSpec, superpowers (brainstorming, writing-plans, test-driven-development, systematic-debugging, verification-before-completion, using-git-worktrees, dispatching-parallel-agents), git
+- CHANGELOG.md | Documents version history and notable changes for a project management and Git repository application
+- Makefile | Provides standardized development commands for managing a Docker-based full-stack application with API, web frontend, database, and testing infrastructure | dep: docker compose, alembic, pytest, ruff, mypy, playwright, npm, postgres, redis
+- README.md | Documentation for a self-hosted development platform that manages projects, git repositories, and development tools with OAuth2 authentication | dep: FastAPI, SQLAlchemy, Pydantic, Alembic, python-jose, React, TypeScript, Vite, React Router, Docker, PostgreSQL, Traefik, Authentik
+- docker-compose.traefik.yml | Deploys a multi-service application (PostgreSQL, Redis, web frontend, API) behind an existing Traefik reverse proxy with TLS termination | dep: docker, docker-compose, traefik, postgres, redis, node/vite, python/fastapi
+- docker-compose.yml | Defines a multi-service Docker Compose stack for a web application with PostgreSQL, Redis, API backend, and web frontend services | dep: Docker, Docker Compose, PostgreSQL, Redis, Vite, asyncpg, Python/FastAPI (implied), Node.js (implied)
+- progress.md | Documents the progress and remaining tasks for a backend-frontend refactoring project involving modularization, code reorganization, and verification.
+- swap-pane | Provides a command to swap the position of two tmux panes within a window or between windows | dep: tmux, client, window, layout, cmd-find, cmd-parse, options
+- ui-audit-spacing-typography.md | A detailed audit report identifying critical CSS styling gaps, mobile layout failures, and design system inconsistencies in a web application's UI components and stylesheets. | dep: React/TSX components, CSS stylesheets (global.css, utilities.css, tokens.css, page-specific CSS), JSX/TSX files in apps/web/src/components and apps/web/src/pages
+- ui-rework-foundations-apply.md | Documents the implementation of Pass 1 (Foundations) of a web UI spacing/typography/visual-rhythm rework, including design token expansion, primitive CSS class additions, component refactors, and OpenSpec documentation. | dep: CSS design tokens, React/TSX components, OpenSpec documentation system, Git/SSH, npm build toolchain
+- ui-rework-pass2-apply.md | Documents the implementation and verification of Pass 2 of a web UI spacing/typography rework, refactoring inline styles into utility classes and design tokens across six components. | dep: CSS custom properties, BEM methodology, utility-first CSS, React/TSX components, OpenSpec documentation system
+## arch
+Contains 13 files.
+## tags
+docker, web, git, application, ui, rework, python, redis
+## symbols
+-
+## workflows
+-
+## dirty
+-

.sisyphus/run-continuation/ses_1da2608b1ffergOzow3NQt1mGr.json

@@ -0,0 +1,10 @@
+{
+  "sessionID": "ses_1da2608b1ffergOzow3NQt1mGr",
+  "updatedAt": "2026-05-15T23:50:42.832Z",
+  "sources": {
+    "background-task": {
+      "state": "idle",
+      "updatedAt": "2026-05-15T23:50:42.832Z"
+    }
+  }
+}

.stoneforge/.pi-map.index.md

@@ -0,0 +1,23 @@
+# .stoneforge (index)
+dir: .stoneforge
+
+## role
+Infrastructure configuration and metadata storage for the Stoneforge tool
+## parent
+index: ./.pi-map.index.md
+map: ./.pi-map.md
+## children
+- .stoneforge/sync
+  index: .stoneforge/sync/.pi-map.index.md
+  map: .stoneforge/sync/.pi-map.md
+## files
+- .dashboard-opened
+- .gitignore
+- config.yaml
+## links
+index: .stoneforge/.pi-map.index.md
+map: .stoneforge/.pi-map.md
+## workflows
+-
+## dirty
+-

.stoneforge/.pi-map.md

@@ -0,0 +1,21 @@
+# .stoneforge
+dir: .stoneforge
+
+index: .stoneforge/.pi-map.index.md
+
+## role
+Infrastructure configuration and metadata storage for the Stoneforge tool
+## files
+- .dashboard-opened | Stores timestamp metadata for tracking when a dashboard was opened
+- .gitignore | Specifies files and patterns for Git to ignore in the repository | dep: git
+- config.yaml | YAML configuration file defining settings for the Stoneforge tool, including database, sync, playbooks, identity, merge, workflow, and agent permissions.
+## arch
+Dot-directory pattern for tool-specific state, using YAML for hierarchical configuration and dotfiles for ephemeral runtime metadata
+## tags
+git, config, stores, timestamp, metadata, tracking, dashboard, was
+## symbols
+-
+## workflows
+-
+## dirty
+-

.stoneforge/sync/.pi-map.index.md

@@ -0,0 +1,20 @@
+# .stoneforge/sync (index)
+dir: .stoneforge/sync
+
+## role
+Provides persistent storage for entity relationships and AI worker agent records in a synchronization system.
+## parent
+index: .stoneforge/.pi-map.index.md
+map: .stoneforge/.pi-map.md
+## children
+-
+## files
+- dependencies.jsonl
+- elements.jsonl
+## links
+index: .stoneforge/sync/.pi-map.index.md
+map: .stoneforge/sync/.pi-map.md
+## workflows
+-
+## dirty
+-

.stoneforge/sync/.pi-map.md

@@ -0,0 +1,20 @@
+# .stoneforge/sync
+dir: .stoneforge/sync
+
+index: .stoneforge/sync/.pi-map.index.md
+
+## role
+Provides persistent storage for entity relationships and AI worker agent records in a synchronization system.
+## files
+- dependencies.jsonl | Stores dependency relationships between entities in JSONL format, including parent-child, blocking, and reply-to relationships with timestamps and creators.
+- elements.jsonl | Stores JSONL-formatted entity records for AI worker agents with their session histories and metadata in a data persistence file.
+## arch
+Append-only JSONL document store with separate files for dependency graph edges (dependencies.jsonl) and entity nodes (elements.jsonl), using a log-structured data pattern for time-ordered, immutable record keeping.
+## tags
+stores, relationships, jsonl, dependencies, elements, dependency, entities, format
+## symbols
+-
+## workflows
+-
+## dirty
+-

AGENTS.md

@@ -4,6 +4,10 @@
 
 OpenSpec is the source of truth. Superpowers is the default workflow. Keep changes small, scoped, and verified.
 
+## Communication
+
+All agent output, code comments, commit messages, documentation, and artifacts must be in **English** unless the user explicitly requests another language.
+
 ## Priority order
 
 1. Current user instruction
@@ -71,6 +75,7 @@ Do not:
 * Introduce new dependencies without clear justification.
 * Treat existing code as more authoritative than OpenSpec for intended behavior.
 * Decide product behavior silently when the spec is unclear.
+* Run `docker compose` commands (build, up, down, etc.) without explicit user approval and proper isolation (e.g., feature branches, separate worktrees, or staged rollouts). Docker Compose operations are deployment-level changes that can affect running services, shared volumes, and network state. Always ask first.
 
 If scope must change, propose an OpenSpec update first.
 

apps/.pi-map.index.md

@@ -0,0 +1,23 @@
+# apps (index)
+dir: apps
+
+## role
+Package apps
+## parent
+index: ./.pi-map.index.md
+map: ./.pi-map.md
+## children
+- apps/api
+  index: apps/api/.pi-map.index.md
+  map: apps/api/.pi-map.md
+- apps/web
+  index: apps/web/.pi-map.index.md
+  map: apps/web/.pi-map.md
+## files
+## links
+index: apps/.pi-map.index.md
+map: apps/.pi-map.md
+## workflows
+-
+## dirty
+-

apps/.pi-map.md

@@ -0,0 +1,18 @@
+# apps
+dir: apps
+
+index: apps/.pi-map.index.md
+
+## role
+Package apps
+## files
+## arch
+Contains 0 files.
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-

apps/api/.dockerignore

@@ -0,0 +1,42 @@
+# Python cache
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Test artifacts
+.pytest_cache/
+.coverage
+htmlcov/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# Git
+.git/
+.gitignore
+
+# Local env files
+.env
+.env.local
+
+# Alembic cache
+alembic/versions/__pycache__/
+
+# Pi lens cache
+.pi-lens/
+
+# Documentation
+docs/
+*.md
+
+# Scripts not needed in container
+scripts/

apps/api/.pi-lens/cache/python-rules-v2.json

@@ -0,0 +1,568 @@
+{
+  "version": "v2",
+  "timestamp": 1779889907001,
+  "ruleHash": "fd9b2b15f2ac8993",
+  "queries": [
+    {
+      "id": "bare-except",
+      "name": "Bare Except Clause",
+      "severity": "warning",
+      "language": "python",
+      "message": "Bare 'except:' clause — catches SystemExit, KeyboardInterrupt",
+      "query": "  (except_clause\n    \"except\") @CLAUSE",
+      "metavars": [
+        "CLAUSE"
+      ],
+      "post_filter": "bare_except_only",
+      "defect_class": "silent-error",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/bare-except.yml"
+    },
+    {
+      "id": "eval-exec",
+      "name": "Eval/Exec Usage",
+      "severity": "warning",
+      "language": "python",
+      "message": "{{FUNC}}() detected — security risk, code injection vulnerability",
+      "query": "  (call\n    function: (identifier) @FUNC\n    (#match? @FUNC \"^(eval|exec)$\")\n    arguments: (argument_list) @ARGS)",
+      "metavars": [
+        "FUNC",
+        "ARGS"
+      ],
+      "defect_class": "injection",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/eval-exec.yml"
+    },
+    {
+      "id": "exit-signature-check",
+      "name": "__exit__ Missing Parameters",
+      "severity": "error",
+      "language": "python",
+      "message": "__exit__ should accept type, value, and traceback arguments",
+      "query": "  (function_definition\n    name: (identifier) @NAME (#eq? @NAME \"__exit__\")\n    parameters: (parameters\n      (_) @SELF\n      . (_) @PARAM1?\n      . (_) @PARAM2?\n      . (_) @PARAM3?))",
+      "metavars": [
+        "NAME",
+        "SELF",
+        "PARAM1",
+        "PARAM2",
+        "PARAM3"
+      ],
+      "post_filter": "exit_params_insufficient",
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/exit-signature-check.yml"
+    },
+    {
+      "id": "in-operator-unsupported",
+      "name": "In and Not In Operators Should Be Used on Valid Objects",
+      "severity": "warning",
+      "language": "python",
+      "message": "'in' operator used on object that may not support containment",
+      "query": "  (comparison_operator\n    (identifier) @OBJ\n    \"in\"\n    (identifier) @TARGET)\n  (comparison_operator\n    (identifier) @OBJ\n    \"not\"\n    \"in\"\n    (identifier) @TARGET)",
+      "metavars": [
+        "OBJ",
+        "TARGET"
+      ],
+      "post_filter": "check_in_operator_types",
+      "defect_class": "correctness",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/in-operator-unsupported.yml"
+    },
+    {
+      "id": "is-vs-equals",
+      "name": "Is vs Equals for Literals",
+      "severity": "warning",
+      "language": "python",
+      "message": "Using 'is' with literal — use '==' for value comparison",
+      "query": "  (comparison_operator\n    (identifier)\n    (\"is\")\n    (string) @LITERAL)\n  (comparison_operator\n    (identifier)\n    (\"is not\")\n    (string) @LITERAL)\n  (comparison_operator\n    (identifier)\n    (\"is\")\n    (integer) @LITERAL)\n  (comparison_operator\n    (identifier)\n    (\"is not\")\n    (integer) @LITERAL)",
+      "metavars": [
+        "LITERAL"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/is-vs-equals.yml"
+    },
+    {
+      "id": "iter-return-iterator",
+      "name": "__iter__ Should Return Iterator",
+      "severity": "warning",
+      "language": "python",
+      "message": "__iter__ should return an iterator (object with __next__ method)",
+      "query": "  (function_definition\n    name: (identifier) @NAME (#eq? @NAME \"__iter__\")\n    body: (block\n      (return_statement) @RETURN))",
+      "metavars": [
+        "NAME",
+        "RETURN"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/iter-return-iterator.yml"
+    },
+    {
+      "id": "mutable-default-arg",
+      "name": "Mutable Default Argument",
+      "severity": "warning",
+      "language": "python",
+      "message": "Mutable default argument — list/dict/set as default value",
+      "query": "  (function_definition\n    (parameters\n      (default_parameter\n        (identifier) @PARAM\n        [(list) (dictionary) (set)] @MUTABLE)))",
+      "metavars": [
+        "PARAM",
+        "MUTABLE"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/mutable-default-arg.yml"
+    },
+    {
+      "id": "no-super-torchscript",
+      "name": "super Should Not Be Used in TorchScript Methods",
+      "severity": "error",
+      "language": "python",
+      "message": "super() calls should not be used in TorchScript methods",
+      "query": "  (function_definition\n    (decorator\n      (call\n        function: (identifier) @DEC (#match? @DEC \"^(torch\\.jit\\.script|jit\\.script)$\")))\n    body: (block\n      (call\n        function: (identifier) @FUNC (#eq? @FUNC \"super\")) @CALL))",
+      "metavars": [
+        "DEC",
+        "FUNC",
+        "CALL"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/no-super-torchscript.yml"
+    },
+    {
+      "id": "notimplemented-boolean-context",
+      "name": "NotImplemented in Boolean Context",
+      "severity": "error",
+      "language": "python",
+      "message": "NotImplemented should not be used in boolean contexts",
+      "query": "  (if_statement\n    condition: (identifier) @COND (#eq? @COND \"NotImplemented\"))\n  (while_statement\n    condition: (identifier) @COND (#eq? @COND \"NotImplemented\"))\n  (binary_operator\n    (identifier) @COND (#eq? @COND \"NotImplemented\")\n    (\"and\" | \"or\"))\n  (boolean_operator\n    (identifier) @COND (#eq? @COND \"NotImplemented\"))\n  (unary_operator\n    operator: (\"not\")\n    argument: (identifier) @COND (#eq? @COND \"NotImplemented\"))",
+      "metavars": [
+        "COND"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/notimplemented-boolean-context.yml"
+    },
+    {
+      "id": "python-assert-production",
+      "name": "Assert in Production Code",
+      "severity": "warning",
+      "language": "python",
+      "message": "assert statement stripped by Python -O flag — use explicit checks with exceptions in production code",
+      "query": "  (assert_statement) @ASSERT",
+      "metavars": [
+        "ASSERT"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-assert-production.yml"
+    },
+    {
+      "id": "python-command-injection",
+      "name": "Command Injection Sink",
+      "severity": "error",
+      "language": "python",
+      "message": "Potential command injection sink — avoid shell execution with dynamic input",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list) @ARGS\n    (#eq? @MOD \"os\")\n    (#match? @FN \"^(system|popen)$\"))\n\n  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list\n      (keyword_argument\n        name: (identifier) @KW\n        value: (true)))\n    (#eq? @MOD \"subprocess\")\n    (#match? @FN \"^(run|Popen|call|check_output|check_call)$\")\n    (#eq? @KW \"shell\"))",
+      "metavars": [
+        "MOD",
+        "FN",
+        "ARGS",
+        "KW"
+      ],
+      "post_filter": "py_command_injection_sink",
+      "defect_class": "injection",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-command-injection.yml"
+    },
+    {
+      "id": "python-cross-language-method",
+      "name": "Cross-Language Method Leakage",
+      "severity": "warning",
+      "language": "python",
+      "message": "'{METHOD}' is not a Python method — likely a {LANG} idiom leaking in",
+      "query": "  (call\n    function: (attribute\n      object: (_) @OBJ\n      attribute: (identifier) @METHOD)\n    (#match? @METHOD \"^(push|forEach|indexOf|charAt|substring|hasOwnProperty|unshift|flatMap|padStart|padEnd|trimStart|trimEnd|equals|isEmpty|println|printf|getClass|hashCode|toCharArray|getBytes|compareTo|equalsIgnoreCase|startsWith|endsWith|each|collect|select|reject|detect|inject|chomp|chop|gsub|upcase|downcase|present|blank|Add|Contains|ToLower|ToUpper|Trim|Substring|WriteLine|ReadLine|TryParse|forEach|includes|assign|freeze|splice|unshift|shift|flatMap)$\"))",
+      "metavars": [
+        "OBJ",
+        "METHOD"
+      ],
+      "post_filter": "match_captures",
+      "post_filter_params": {
+        "METHOD": "^(push|forEach|indexOf|charAt|substring|hasOwnProperty|unshift|flatMap|padStart|padEnd|trimStart|trimEnd|equals|isEmpty|println|printf|getClass|hashCode|toCharArray|getBytes|compareTo|equalsIgnoreCase|startsWith|endsWith|each|collect|select|reject|detect|inject|chomp|chop|gsub|upcase|downcase|present|blank|Add|Contains|ToLower|ToUpper|Trim|Substring|WriteLine|ReadLine|TryParse|forEach|includes|assign|freeze|splice|unshift|shift|flatMap)$"
+      },
+      "defect_class": "hallucination",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-cross-language-method.yml"
+    },
+    {
+      "id": "python-debugger",
+      "name": "Debugger Statement",
+      "severity": "warning",
+      "language": "python",
+      "message": "Debugger call '{{FUNC}}' — remove before committing",
+      "query": "  (call\n    function: (identifier) @FUNC\n    (#eq? @FUNC \"breakpoint\"))\n\n  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FUNC)\n    (#eq? @MOD \"pdb\")\n    (#match? @FUNC \"^(set_trace|post_mortem|pm|run|runcall)$\"))",
+      "metavars": [
+        "FUNC",
+        "MOD"
+      ],
+      "defect_class": "safety",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-debugger.yml"
+    },
+    {
+      "id": "python-empty-except",
+      "name": "Empty Except Block",
+      "severity": "warning",
+      "language": "python",
+      "message": "Except block only contains 'pass' — handle or re-raise the exception",
+      "query": "  (try_statement\n    (except_clause\n      body: (block) @BODY))",
+      "metavars": [
+        "BODY"
+      ],
+      "post_filter": "python_empty_except",
+      "defect_class": "silent-error",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-empty-except.yml"
+    },
+    {
+      "id": "python-hallucinated-import",
+      "name": "Hallucinated Import",
+      "severity": "warning",
+      "language": "python",
+      "message": "Hallucinated import — '{NAME}' does not exist in '{MODULE}'",
+      "query": "  (import_from_statement\n    module_name: (dotted_name) @MODULE\n    name: (dotted_name) @NAME)",
+      "metavars": [
+        "MODULE",
+        "NAME"
+      ],
+      "post_filter": "match_captures",
+      "post_filter_params": {
+        "MODULE": "^(requests|flask|django|typing|collections|asyncio|json|unittest|pytest|urllib|sqlalchemy)$",
+        "NAME": "^(JSONResponse|HTMLResponse|RedirectResponse|StreamingResponse|Depends|Query|Path|Body|Header|Cookie|Form|File|UploadFile|FastAPI|APIRouter|HTTPException|BackgroundTasks|dataclass|fields|BaseModel|Field|validator|aiohttp|parse|stringify|fixture|TestCase|get|post|put|delete|Model|Session|Column|Integer|String)$"
+      },
+      "defect_class": "hallucination",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-hallucinated-import.yml"
+    },
+    {
+      "id": "python-hardcoded-secrets",
+      "name": "Hardcoded Secret",
+      "severity": "warning",
+      "language": "python",
+      "message": "Hardcoded {{VARNAME}} — use environment variables or a secrets manager",
+      "query": "  (assignment\n    left: (identifier) @VARNAME\n    right: (string) @VALUE)",
+      "metavars": [
+        "VARNAME",
+        "VALUE"
+      ],
+      "post_filter": "check_secret_pattern",
+      "defect_class": "secrets",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-hardcoded-secrets.yml"
+    },
+    {
+      "id": "python-insecure-deserialization",
+      "name": "Insecure Deserialization",
+      "severity": "error",
+      "language": "python",
+      "message": "Potential insecure deserialization sink — avoid unsafe loaders",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list (_) @DATA)\n    (#match? @MOD \"^(pickle|yaml)$\")\n    (#match? @FN \"^(load|loads|unsafe_load)$\"))",
+      "metavars": [
+        "MOD",
+        "FN",
+        "DATA"
+      ],
+      "post_filter": "py_insecure_deserialization_sink",
+      "defect_class": "injection",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-insecure-deserialization.yml"
+    },
+    {
+      "id": "python-insecure-random",
+      "name": "Insecure Randomness",
+      "severity": "warning",
+      "language": "python",
+      "message": "Insecure randomness source detected — use secrets or os.urandom for security-sensitive values",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list) @ARGS\n    (#eq? @MOD \"random\")\n    (#match? @FN \"^(random|randint|randrange|choice|choices)$\"))",
+      "metavars": [
+        "MOD",
+        "FN",
+        "ARGS"
+      ],
+      "defect_class": "injection",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-insecure-random.yml"
+    },
+    {
+      "id": "python-mutable-class-attr",
+      "name": "Mutable Class Attribute",
+      "severity": "warning",
+      "language": "python",
+      "message": "Class attribute '{{VARNAME}}' is mutable — shared across all instances",
+      "query": "  (class_definition\n    body: (block\n      (expression_statement\n        (assignment\n          left: (identifier) @VARNAME\n          right: [\n            (list) @VALUE\n            (dictionary) @VALUE\n            (set) @VALUE\n          ]))))",
+      "metavars": [
+        "VARNAME",
+        "VALUE"
+      ],
+      "post_filter": "not_in_function",
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-mutable-class-attr.yml"
+    },
+    {
+      "id": "python-path-traversal",
+      "name": "Path Traversal Risk",
+      "severity": "warning",
+      "language": "python",
+      "message": "Potential path traversal sink — sanitize and constrain file paths",
+      "query": "  [\n    (call\n      function: (identifier) @FN\n      arguments: (argument_list\n        [(identifier) (binary_operator) (call)] @PATH))\n    (call\n      function: (attribute\n        object: (identifier) @MOD\n        attribute: (identifier) @FN)\n      arguments: (argument_list\n        [(identifier) (binary_operator) (call)] @PATH))\n  ]\n  (#match? @FN \"^(open|read_text|read_bytes|write_text|write_bytes|remove|unlink|rmdir)$\")",
+      "metavars": [
+        "MOD",
+        "FN",
+        "PATH"
+      ],
+      "post_filter": "py_path_traversal_sink",
+      "defect_class": "injection",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-path-traversal.yml"
+    },
+    {
+      "id": "python-print-statement",
+      "name": "Print Statement in Production",
+      "severity": "warning",
+      "language": "python",
+      "message": "print() — remove debug output before committing",
+      "query": "  (call\n    function: (identifier) @FUNC\n    (#eq? @FUNC \"print\")\n    arguments: (argument_list) @ARGS)",
+      "metavars": [
+        "FUNC",
+        "ARGS"
+      ],
+      "post_filter": "not_in_test_block",
+      "defect_class": "safety",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-print-statement.yml"
+    },
+    {
+      "id": "python-raise-string",
+      "name": "Raise String Instead of Exception",
+      "severity": "warning",
+      "language": "python",
+      "message": "raise with string literal — Python 3 requires exception instances",
+      "query": "  (raise_statement\n    (string) @VALUE)",
+      "metavars": [
+        "VALUE"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-raise-string.yml"
+    },
+    {
+      "id": "python-sleep-in-test",
+      "name": "time.sleep in Test",
+      "severity": "warning",
+      "language": "python",
+      "message": "time.sleep() in test — use synchronisation primitives or polling helpers instead of fixed sleeps",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    (#eq? @MOD \"time\")\n    (#eq? @FN \"sleep\")) @CALL",
+      "metavars": [
+        "MOD",
+        "FN",
+        "CALL"
+      ],
+      "defect_class": "async-misuse",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-sleep-in-test.yml"
+    },
+    {
+      "id": "python-sql-injection",
+      "name": "SQL Injection Risk",
+      "severity": "error",
+      "language": "python",
+      "message": "Potential SQL injection sink — use parameterized queries",
+      "query": "  (call\n    function: (attribute\n      object: (_) @OBJ\n      attribute: (identifier) @FN)\n    arguments: (argument_list\n      [(binary_operator) (identifier) (call)] @SQL\n      (_)*))",
+      "metavars": [
+        "OBJ",
+        "FN",
+        "SQL"
+      ],
+      "post_filter": "py_sql_injection_sink",
+      "defect_class": "injection",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-sql-injection.yml"
+    },
+    {
+      "id": "python-ssrf",
+      "name": "SSRF Risk",
+      "severity": "warning",
+      "language": "python",
+      "message": "Potential SSRF sink — validate/allowlist outbound URLs",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list\n      [(identifier) (subscript) (call)] @URL)\n    (#eq? @MOD \"requests\")\n    (#match? @FN \"^(get|post|put|patch|delete|request|head|options)$\"))",
+      "metavars": [
+        "MOD",
+        "FN",
+        "URL"
+      ],
+      "post_filter": "py_ssrf_sink",
+      "defect_class": "injection",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-ssrf.yml"
+    },
+    {
+      "id": "python-subprocess-shell",
+      "name": "subprocess with shell=True",
+      "severity": "warning",
+      "language": "python",
+      "message": "subprocess called with shell=True — command injection risk if any argument is user-controlled",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list\n      (keyword_argument\n        name: (identifier) @KW\n        value: (true) @VAL))\n    (#eq? @MOD \"subprocess\")\n    (#match? @FN \"^(run|Popen|call|check_output|check_call)$\")\n    (#eq? @KW \"shell\"))",
+      "metavars": [
+        "MOD",
+        "FN",
+        "KW"
+      ],
+      "defect_class": "injection",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-subprocess-shell.yml"
+    },
+    {
+      "id": "python-thread-global-write",
+      "name": "Threaded Shared State Risk",
+      "severity": "warning",
+      "language": "python",
+      "message": "Thread creation detected — ensure shared state mutations are synchronized",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list) @ARGS)\n  (#eq? @MOD \"threading\")\n  (#eq? @FN \"Thread\")",
+      "metavars": [
+        "MOD",
+        "FN",
+        "ARGS"
+      ],
+      "defect_class": "async-misuse",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-thread-global-write.yml"
+    },
+    {
+      "id": "python-unsafe-regex",
+      "name": "Unsafe Dynamic Regex",
+      "severity": "warning",
+      "language": "python",
+      "message": "re.{{FUNC}}() with variable pattern — ReDoS risk if pattern is user-controlled",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FUNC)\n    arguments: (argument_list\n      (identifier) @PATTERN)\n    (#eq? @MOD \"re\")\n    (#match? @FUNC \"^(compile|match|search|fullmatch|findall|finditer|sub|subn|split)$\"))",
+      "metavars": [
+        "MOD",
+        "FUNC",
+        "PATTERN"
+      ],
+      "defect_class": "injection",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-unsafe-regex.yml"
+    },
+    {
+      "id": "python-weak-hash",
+      "name": "Weak Hash Primitive",
+      "severity": "error",
+      "language": "python",
+      "message": "Weak hash primitive detected (MD5/SHA1) — use SHA-256+ for security-sensitive contexts",
+      "query": "  (call\n    function: (attribute\n      object: (identifier) @MOD\n      attribute: (identifier) @FN)\n    arguments: (argument_list) @ARGS\n    (#eq? @MOD \"hashlib\")\n    (#match? @FN \"^(md5|sha1)$\"))",
+      "metavars": [
+        "MOD",
+        "FN",
+        "ARGS"
+      ],
+      "defect_class": "injection",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/python-weak-hash.yml"
+    },
+    {
+      "id": "return-in-generator",
+      "name": "Return with Value in Generator",
+      "severity": "error",
+      "language": "python",
+      "message": "'return' with a value should not be used in a generator function",
+      "query": "  (function_definition\n    body: (block\n      (return_statement\n        (_) @RETURN_VAL) @RETURN)) @FUNCTION",
+      "metavars": [
+        "FUNCTION",
+        "RETURN",
+        "RETURN_VAL"
+      ],
+      "post_filter": "is_generator_with_valued_return",
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/return-in-generator.yml"
+    },
+    {
+      "id": "return-in-init",
+      "name": "Return Value in __init__",
+      "severity": "error",
+      "language": "python",
+      "message": "__init__ should not return a value — it must always return None",
+      "query": "  (function_definition\n    name: (identifier) @NAME (#eq? @NAME \"__init__\")\n    body: (block\n      (return_statement\n        (_) @RETURN_VAL) @RETURN))",
+      "metavars": [
+        "NAME",
+        "RETURN",
+        "RETURN_VAL"
+      ],
+      "post_filter": "has_return_value",
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/return-in-init.yml"
+    },
+    {
+      "id": "send-file-mimetype",
+      "name": "send_file Should Specify Mimetype or Download Name",
+      "severity": "error",
+      "language": "python",
+      "message": "send_file should specify 'mimetype' or 'download_name' when used with file-like objects",
+      "query": "  (call\n    function: (identifier) @FUNC (#eq? @FUNC \"send_file\")\n    arguments: (argument_list\n      (_) @FIRST_ARG\n      (keyword_argument)? @KW))",
+      "metavars": [
+        "FUNC",
+        "FIRST_ARG",
+        "KW"
+      ],
+      "post_filter": "missing_mimetype_and_download_name",
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/send-file-mimetype.yml"
+    },
+    {
+      "id": "unreachable-except",
+      "name": "Unreachable Except Clause",
+      "severity": "warning",
+      "language": "python",
+      "message": "Unreachable except clause — earlier except catches all",
+      "query": "  (try_statement\n    (except_clause\n      \"except\") @GENERAL\n    (except_clause\n      \"except\"\n      (identifier) @SPECIFIC))",
+      "metavars": [
+        "GENERAL",
+        "SPECIFIC"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/unreachable-except.yml"
+    },
+    {
+      "id": "wildcard-import",
+      "name": "Wildcard Import",
+      "severity": "warning",
+      "language": "python",
+      "message": "Wildcard import — pollutes namespace, hard to track origin",
+      "query": "  (import_from_statement\n    module_name: (dotted_name) @MODULE\n    (wildcard_import) @WILDCARD)",
+      "metavars": [
+        "MODULE",
+        "WILDCARD"
+      ],
+      "defect_class": "safety",
+      "inline_tier": "warning",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/wildcard-import.yml"
+    },
+    {
+      "id": "yield-return-outside-function",
+      "name": "Yield/Return Outside Function",
+      "severity": "error",
+      "language": "python",
+      "message": "{{STATEMENT}} used outside function — syntax error",
+      "query": "  (module\n    (expression_statement\n      (yield) @STATEMENT))\n  (module\n    (expression_statement\n      (yield_expression) @STATEMENT))\n  (module\n    (return_statement) @STATEMENT)",
+      "metavars": [
+        "STATEMENT"
+      ],
+      "defect_class": "correctness",
+      "inline_tier": "blocking",
+      "filePath": "/home/alex/.npm-global/lib/node_modules/pi-lens/rules/tree-sitter-queries/python/yield-return-outside-function.yml"
+    }
+  ]
+}

apps/api/.pi-map.index.md

@@ -0,0 +1,54 @@
+# apps/api (index)
+dir: apps/api
+
+## role
+Backend API server for the Headquarter platform, providing self-hosted project management, git repository management, and development tool orchestration services.
+## parent
+index: apps/.pi-map.index.md
+map: apps/.pi-map.md
+## children
+- apps/api/.mypy_cache
+  index: apps/api/.mypy_cache/.pi-map.index.md
+  map: apps/api/.mypy_cache/.pi-map.md
+- apps/api/.pi-lens
+  index: apps/api/.pi-lens/.pi-map.index.md
+  map: apps/api/.pi-lens/.pi-map.md
+- apps/api/.pytest_cache
+  index: apps/api/.pytest_cache/.pi-map.index.md
+  map: apps/api/.pytest_cache/.pi-map.md
+- apps/api/.ruff_cache
+  index: apps/api/.ruff_cache/.pi-map.index.md
+  map: apps/api/.ruff_cache/.pi-map.md
+- apps/api/alembic
+  index: apps/api/alembic/.pi-map.index.md
+  map: apps/api/alembic/.pi-map.md
+- apps/api/app
+  index: apps/api/app/.pi-map.index.md
+  map: apps/api/app/.pi-map.md
+- apps/api/headquarter_api.egg-info
+  index: apps/api/headquarter_api.egg-info/.pi-map.index.md
+  map: apps/api/headquarter_api.egg-info/.pi-map.md
+- apps/api/src
+  index: apps/api/src/.pi-map.index.md
+  map: apps/api/src/.pi-map.md
+- apps/api/tests
+  index: apps/api/tests/.pi-map.index.md
+  map: apps/api/tests/.pi-map.md
+- apps/api/uploads
+  index: apps/api/uploads/.pi-map.index.md
+  map: apps/api/uploads/.pi-map.md
+## files
+- .dockerignore
+- Dockerfile
+- README.md
+- alembic.ini
+- pyproject.toml
+- uv.lock
+- wait-for-db.sh
+## links
+index: apps/api/.pi-map.index.md
+map: apps/api/.pi-map.md
+## workflows
+-
+## dirty
+-

apps/api/.pi-map.md

@@ -0,0 +1,25 @@
+# apps/api
+dir: apps/api
+
+index: apps/api/.pi-map.index.md
+
+## role
+Backend API server for the Headquarter platform, providing self-hosted project management, git repository management, and development tool orchestration services.
+## files
+- .dockerignore | Specifies files and directories to exclude from the Docker build context to optimize image build times and prevent sensitive or unnecessary files from being included.
+- Dockerfile | Multi-stage Dockerfile that builds and runs a Python application with Docker CLI access, cloudflared, and database readiness checks. | dep: python:3.11-slim, libpq5, git, openssh-client, docker-ce-cli, docker-compose-plugin, cloudflared, uvicorn, netcat-openbsd
+- README.md | Provides comprehensive documentation for the Headquarter API, a self-hosted platform for managing projects, git repositories, and development tools. | dep: FastAPI, SQLAlchemy, PostgreSQL, asyncpg, Alembic, Docker, Authentik, Pydantic, Ruff, mypy, pytest
+- alembic.ini | Configuration file for Alembic database migration tool, defining database connection and logging settings. | dep: alembic, sqlalchemy, asyncpg, postgresql
+- pyproject.toml | Defines project metadata, dependencies, and tool configuration for the Headquarter platform API. | dep: fastapi, uvicorn, sqlalchemy, asyncpg, alembic, pydantic, pydantic-settings, httpx, structlog, cryptography, pytest, mypy, ruff
+- uv.lock | This file is a UV lockfile that pins exact versions, hashes, and metadata for all Python project dependencies to ensure reproducible environments. | dep: uv, aiosqlite, alembic, annotated-types, anyio, asyncpg, sqlalchemy, mako
+- wait-for-db.sh | Polls a PostgreSQL host/port until it is available or a retry limit is reached, then executes the passed command. | dep: nc, sleep
+## arch
+Modern Python async API using FastAPI/Starlette with SQLAlchemy ORM, Alembic migrations, multi-stage Docker containerization with cloudflared tunneling, UV package management, and PostgreSQL database with health-checked startup orchestration.
+## tags
+alembic, docker, sqlalchemy, asyncpg, dockerfile, database, postgresql, pydantic
+## symbols
+-
+## workflows
+-
+## dirty
+-

apps/api/Dockerfile

@@ -50,8 +50,8 @@ ENV PATH=/root/.local/bin:$PATH
 # Copy application code
 COPY --chown=appuser:appgroup . .
 
-# Create directories for repo and instance storage
-RUN mkdir -p /data/repos /data/instances && chown -R appuser:appgroup /data
+# Create directories for repo, instance, and workspace storage
+RUN mkdir -p /data/repos /data/instances /data/working-copies && chown -R appuser:appgroup /data
 
 # Copy wait-for-db script
 COPY wait-for-db.sh /usr/local/bin/wait-for-db.sh

apps/api/alembic/.pi-map.index.md

@@ -0,0 +1,25 @@
+# apps/api/alembic (index)
+dir: apps/api/alembic
+
+## role
+Database migration tooling for the API service, enabling version-controlled schema changes with async SQLAlchemy support.
+## parent
+index: apps/api/.pi-map.index.md
+map: apps/api/.pi-map.md
+## children
+- apps/api/alembic/versions
+  index: apps/api/alembic/versions/.pi-map.index.md
+  map: apps/api/alembic/versions/.pi-map.md
+## files
+- env.py
+- script.py.mako
+## links
+index: apps/api/alembic/.pi-map.index.md
+map: apps/api/alembic/.pi-map.md
+## workflows
+- change alembic behavior
+  read: env.py, script.py.mako
+- explore alembic subdirectories
+  index: apps/api/alembic/versions/.pi-map.index.md
+## dirty
+-

apps/api/alembic/.pi-map.md

@@ -0,0 +1,30 @@
+# apps/api/alembic
+dir: apps/api/alembic
+
+index: apps/api/alembic/.pi-map.index.md
+
+## role
+Database migration tooling for the API service, enabling version-controlled schema changes with async SQLAlchemy support.
+## files
+- env.py | Configures Alembic database migration environment with async SQLAlchemy support. | exp: func:run_migrations_offline() → None, call:context.configure, call:context.begin_transaction, call:context.run_migrations, func:do_run_migrations(connection: Connection) → None, call:context.configure, call:context.begin_transaction, call:context.run_migrations, func:run_async_migrations() → None, call:async_engine_from_config, call:config.get_section, call:connectable.connect, call:connection.run_sync, call:connectable.dispose, func:run_migrations_online() → None, call:asyncio.run, call:run_async_migrations | dep: logging.config, alembic, sqlalchemy, sqlalchemy.engine, sqlalchemy.ext.asyncio, src.config, src.models, asyncio
+- script.py.mako | Alembic database migration script template that generates Python migration files for SQLAlchemy database schema changes | dep: alembic, sqlalchemy, mako
+## arch
+Template-based migration generation using Alembic's standard env.py configuration pattern with async SQLAlchemy engine integration and Mako templating for migration script scaffolding.
+## tags
+migrations, run, sqlalchemy, async, alembic, call:context.configure, call:context.begin, transaction
+## symbols
+- run_migrations_offline
+- do_run_migrations
+- run_async_migrations
+- run_migrations_online
+- call:context.configure
+- call:context.begin_transaction
+- call:context.run_migrations
+- call:async_engine_from_config
+## workflows
+- change alembic behavior
+  read: env.py, script.py.mako
+- explore alembic subdirectories
+  index: apps/api/alembic/versions/.pi-map.index.md
+## dirty
+-

apps/api/alembic/versions/.pi-map.index.md

@@ -0,0 +1,78 @@
+# apps/api/alembic/versions (index)
+dir: apps/api/alembic/versions
+
+## role
+Database schema versioning and incremental migration management for the API's relational data model using Alembic.
+## parent
+index: apps/api/alembic/.pi-map.index.md
+map: apps/api/alembic/.pi-map.md
+## children
+- apps/api/alembic/versions/.ruff_cache
+  index: apps/api/alembic/versions/.ruff_cache/.pi-map.index.md
+  map: apps/api/alembic/versions/.ruff_cache/.pi-map.md
+## files
+- 0001_initial_schema.py
+- 0002_refresh_tokens.py
+- 0003_user_configs.py
+- 0004_tool_types.py
+- 0005_ssh_keys_timestamps.py
+- 0006_tool_instances.py
+- 0007_instance_container_name.py
+- 0008_tool_type_category.py
+- 0009_tool_configs.py
+- 0010_tool_type_default_port.py
+- 0011_tool_instance_tunnel_fields.py
+- 0012_default_port_req.py
+- 0013_add_config_profiles.py
+- 0013_add_probe_result.py
+- 0014_add_profile_resolver_fields.py
+- 0014_merge_heads.py
+- 0015_single_interface.py
+- 069d3da4dc9b_add_ssh_key_id_to_config_profiles.py
+- 20260527160017_add_pi_agent_tool_type.py
+- 2026_05_22_add_clone_mode.py
+- 2026_05_23_remove_is_builtin.py
+- 2026_05_24_220141_add_startup_command.py
+- 2026_05_24_add_config_profiles.py
+- 2026_05_26_add_git_mounts.py
+- 2026_05_27_external_repos.py
+- 2026_05_28_add_monitoring_tables.py
+- 2026_05_28_add_terminal_sessions_table.py
+- 2026_05_28_add_tool_definition_manifests.py
+- 2026_05_28_drop_tool_configs_and_config_folders.py
+- 2026_05_29_add_notifications_table.py
+- 2026_05_29_add_ssh_key_ids_to_tool_instances.py
+- 2026_05_29_drop_ssh_key_id_from_config_profiles.py
+- 2026_05_29_fix_code_server_bind_addr.py
+- 2026_05_29_fix_code_server_bind_addr_port.py
+- 2026_05_29_fix_web_tool_bind_address.py
+- 2026_05_29_remove_lsio_command_override.py
+- 2026_05_29_remove_ssh_keys_mount_from_manifest.py
+- 2026_06_01_add_workspaces.py
+- 2026_06_13_make_clone_mode_nullable.py
+- 2026_06_14_104415_add_tool_type_home_directory.py
+- 2026_06_14_182955_fix_pi_agent_home_directory_mount.py
+- 2026_06_15_090500_remove_pi_agent_explicit_repo_mount.py
+- 2026_06_19_113000_remove_pi_agent_workspace_symlink.py
+- 398082499c30_add_tool_config_fields.py
+- 6fc7bfcf199f_merge_remove_is_builtin_and_add_config_.py
+- 86cec91fdb00_merge_profile_resolver_and_workspaces_.py
+- 8c6d1dbd4798_remove_pi_config_and_state_mounts_from_.py
+- 8ed7dd80973d_create_config_folders_table.py
+- af8512103d67_add_tool_type_fields.py
+- f3d2dc90ba3a_merge_single_interface_and_clone_mode.py
+- fc8f1a20cbf6_merge_home_directory_and_pi_agent_mount_.py
+## links
+index: apps/api/alembic/versions/.pi-map.index.md
+map: apps/api/alembic/versions/.pi-map.md
+## workflows
+- change versions behavior
+  read: 0001_initial_schema.py, 0002_refresh_tokens.py, 0003_user_configs.py
+- change versions CLI
+  read: 2026_05_24_220141_add_startup_command.py, 2026_05_29_remove_lsio_command_override.py
+- change versions config
+  read: 0003_user_configs.py, 0009_tool_configs.py, 0013_add_config_profiles.py
+- explore versions subdirectories
+  index: apps/api/alembic/versions/.ruff_cache/.pi-map.index.md
+## dirty
+-

apps/api/alembic/versions/.pi-map.md

@@ -0,0 +1,83 @@
+# apps/api/alembic/versions
+dir: apps/api/alembic/versions
+
+index: apps/api/alembic/versions/.pi-map.index.md
+
+## role
+Database schema versioning and incremental migration management for the API's relational data model using Alembic.
+## files
+- 0001_initial_schema.py | Alembic database migration that creates the initial schema with five tables (users, ssh_keys, projects, git_repositories, user_configs) for a Git/SSH management application. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.String, call:postgresql.UUID, call:sa.DateTime, call:sa.func.now, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, call:op.create_index, call:op.f, call:sa.Text, call:sa.ForeignKeyConstraint, call:sa.Boolean, call:postgresql.JSONB, func:downgrade() → None, call:op.drop_table, call:op.drop_index, call:op.f | dep: alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 0002_refresh_tokens.py | Alembic database migration that creates a refresh_tokens table with indexes for secure session management | exp: func:upgrade() → None, call:op.get_bind, call:sa.inspect, call:inspector.has_table, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.String, call:sa.DateTime, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, call:inspector.get_indexes, call:op.f, call:op.create_index, func:downgrade() → None, call:op.get_bind, call:sa.inspect, call:inspector.has_table, call:inspector.get_indexes, call:op.f, call:op.drop_index, call:op.drop_table | dep: alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 0003_user_configs.py | Alembic database migration that creates a user_configs table with JSON configuration storage per user | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.UUID, call:sa.JSON, call:sa.DateTime, call:sa.text, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, func:downgrade() → None, call:op.drop_table | dep: typing, alembic, sqlalchemy
+- 0004_tool_types.py | Alembic database migration that creates a tool_types table with metadata, templates, and user tracking fields | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.Uuid, call:sa.String, call:sa.Text, call:sa.JSON, call:sa.Boolean, call:sa.ForeignKey, call:sa.DateTime, call:sa.text, func:downgrade() → None, call:op.drop_table | dep: typing, alembic, sqlalchemy
+- 0005_ssh_keys_timestamps.py | Alembic database migration that adds created_at and updated_at timestamp columns to the ssh_keys table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.DateTime, call:sa.text, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy
+- 0006_tool_instances.py | Alembic database migration that creates a tool_instances table with foreign key relationships to tool_types, git_repositories, projects, and users tables, plus indexes for common query patterns. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.text, call:sa.String, call:sa.Integer, call:sa.DateTime, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: typing, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 0007_instance_container_name.py | Alembic database migration that adds a nullable container_name column to the tool_instances table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.String, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy
+- 0008_tool_type_category.py | Alembic database migration that adds `category` and `interfaces` columns to the `tool_types` table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.String, call:sa.JSON, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy
+- 0009_tool_configs.py | Alembic database migration that creates a tool_configs table with UUID primary keys, foreign keys to users/tool_types/projects, key-value configuration storage, and supporting indexes. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.text, call:sa.String, call:sa.Text, call:sa.DateTime, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: typing, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 0010_tool_type_default_port.py | Alembic database migration that adds a nullable default_port column to the tool_types table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.Integer, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy
+- 0011_tool_instance_tunnel_fields.py | Alembic database migration that adds tunnel-related fields (public_url and tunnel_id) to the tool_instances table. | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.String, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy
+- 0012_default_port_req.py | Alembic database migration that populates default_port values for existing tool types and makes the column non-nullable | exp: func:upgrade() → None, call:op.execute, call:op.alter_column, call:sa.Integer, func:downgrade() → None, call:op.alter_column, call:sa.Integer | dep: typing, alembic, sqlalchemy
+- 0013_add_config_profiles.py | Alembic database migration that adds config_profiles, config_includes, config_mounts tables and a selected_profile_id column to tool_instances with defensive checks for idempotent execution | exp: func:_table_exists(table_name: str) → bool, call:sa.inspect(op.get_bind()).has_table, call:op.get_bind, func:_column_exists(table_name: str, column_name: str) → bool, call:_table_exists, call:sa.inspect(op.get_bind()).get_columns, call:op.get_bind, func:_index_exists(table_name: str, index_name: str) → bool, call:_table_exists, call:sa.inspect(op.get_bind()).get_indexes, call:op.get_bind, func:_foreign_key_exists(table_name: str, constrained_columns: list[str], referred_table: str) → bool, call:_table_exists, call:sa.inspect(op.get_bind()).get_foreign_keys, call:op.get_bind, call:foreign_key.get, func:upgrade() → None, call:_table_exists, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.String, call:sa.Text, call:sa.DateTime, call:sa.text, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, call:_index_exists, call:op.create_index, call:sa.Integer, call:_column_exists, call:op.add_column, call:_foreign_key_exists, call:op.create_foreign_key, func:downgrade() → None, call:op.drop_index, call:op.drop_constraint, call:op.drop_column, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 0013_add_probe_result.py | Database migration to add a JSON probe_result column to the tool_instances table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 0014_add_profile_resolver_fields.py | Alembic database migration that adds profile resolver fields to config_profiles and config_mounts tables with idempotent schema checks | exp: func:_table_exists(table_name: str) → bool, call:sa.inspect(op.get_bind()).has_table, call:op.get_bind, func:_column_exists(table_name: str, column_name: str) → bool, call:_table_exists, call:sa.inspect(op.get_bind()).get_columns, call:op.get_bind, func:_index_exists(table_name: str, index_name: str) → bool, call:_table_exists, call:sa.inspect(op.get_bind()).get_indexes, call:op.get_bind, func:_foreign_key_exists(table_name: str, constrained_columns: list[str], referred_table: str) → bool, call:_table_exists, call:sa.inspect(op.get_bind()).get_foreign_keys, call:op.get_bind, call:foreign_key.get, func:_foreign_key_names_for_column(table_name: str, column_name: str) → list[str], call:_table_exists, call:sa.inspect(op.get_bind()).get_foreign_keys, call:op.get_bind, call:foreign_key.get, call:names.append, func:upgrade() → None, call:_column_exists, call:op.add_column, call:sa.Column, call:postgresql.UUID, call:sa.JSON, call:sa.Text, call:sa.Integer, call:sa.Boolean, call:_foreign_key_exists, call:op.create_foreign_key, call:_index_exists, call:op.create_index, call:op.alter_column, call:sa.String, call:_foreign_key_names_for_column, call:op.drop_constraint, call:op.drop_column, func:downgrade() → None, call:op.add_column, call:sa.Column, call:postgresql.UUID, call:sa.Text, call:op.drop_column, call:op.alter_column, call:op.drop_index, call:op.drop_constraint | dep: collections.abc, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 0014_merge_heads.py | Alembic merge migration that reconciles two divergent migration branches without applying schema changes | exp: func:upgrade() → None, func:downgrade() → None | dep: typing, alembic
+- 0015_single_interface.py | Alembic database migration that replaces a JSON array `interfaces` column with a single `interface_type` string column and adds a `requires_port` boolean column, with dialect-specific SQL for PostgreSQL and SQLite data migration. | exp: func:_get_dialect() → str, call:op.get_bind, func:upgrade() → None, call:_get_dialect, call:op.add_column, call:sa.Column, call:sa.String, call:sa.Boolean, call:op.execute, call:op.alter_column, call:op.drop_column, call:op.create_check_constraint, call:sa.text, func:downgrade() → None, call:_get_dialect, call:op.drop_constraint, call:op.add_column, call:sa.Column, call:postgresql.JSONB, call:sa.Text, call:op.execute, call:sa.JSON, call:op.drop_column | dep: typing, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 069d3da4dc9b_add_ssh_key_id_to_config_profiles.py | Alembic database migration that adds an ssh_key_id foreign key column to the config_profiles table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.Uuid, call:sa.ForeignKey, func:downgrade() → None, call:op.drop_column | dep: alembic, sqlalchemy
+- 20260527160017_add_pi_agent_tool_type.py | Adds a database migration that inserts a new "pi-agent" tool type into a tool_types table, defining a terminal-based Docker development environment with nvim, ranger, and tmux. | exp: func:upgrade() → None, call:op.get_bind, call:conn.execute( sa.text("SELECT id FROM tool_types WHERE name = 'pi-agent'") ).fetchone, call:sa.text, call:json.dumps, func:downgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text | dep: json, typing, alembic, uuid, sqlalchemy
+- 2026_05_22_add_clone_mode.py | Alembic database migration that adds ssh_key_id foreign key to git_repositories table and clone_mode/branch columns to tool_instances table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:postgresql.UUID, call:op.create_foreign_key, call:sa.String, func:downgrade() → None, call:op.drop_column, call:op.drop_constraint | dep: alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 2026_05_23_remove_is_builtin.py | Alembic database migration that removes the `is_builtin` column from the `tool_types` table with a downgrade path to restore it. | exp: func:upgrade() → None, call:op.execute, func:downgrade() → None, call:op.add_column, call:sa.Column, call:sa.Boolean | dep: alembic, sqlalchemy
+- 2026_05_24_220141_add_startup_command.py | Alembic database migration that adds a nullable startup_command column to the tool_types table. | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.Text, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy
+- 2026_05_24_add_config_profiles.py | Alembic database migration that creates config_profiles and config_profile_includes tables with indexes, and adds a selected_config_profile_id foreign key to tool_instances. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.text, call:sa.ForeignKey, call:sa.String, call:sa.Text, call:postgresql.JSONB, call:sa.Boolean, call:sa.DateTime, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, call:op.create_index, call:sa.Integer, call:op.add_column, func:downgrade() → None, call:op.drop_index, call:op.drop_column, call:op.drop_table | dep: typing, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 2026_05_26_add_git_mounts.py | Database migration to add a `git_mounts` JSON column to the `config_profiles` table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.JSON, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy
+- 2026_05_27_external_repos.py | Alembic database migration that makes project_id nullable in git_repositories table to support external repositories and expands alembic_version version_num column to VARCHAR(64). | exp: func:upgrade() → None, call:op.execute, call:op.alter_column, call:sa.UUID, func:downgrade() → None, call:op.alter_column, call:sa.UUID, call:op.execute | dep: typing, alembic, sqlalchemy
+- 2026_05_28_add_monitoring_tables.py | Creates two database tables (instance_events and health_checks) for monitoring tool instances via an Alembic migration. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.Uuid, call:sa.String, call:sa.Text, call:sa.JSON, call:sa.DateTime, call:sa.func.now, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, call:sa.Boolean, call:sa.Integer, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy
+- 2026_05_28_add_terminal_sessions_table.py | Alembic database migration that creates a terminal_sessions table with foreign key to tool_instances, including indexes and audit timestamps | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.UUID, call:sa.String, call:sa.DateTime, call:sa.text, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, call:op.f, func:downgrade() → None, call:op.drop_index, call:op.f, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy
+- 2026_05_28_add_tool_definition_manifests.py | Alembic database migration that creates a tool_definition_manifests table, adds manifest support to tool_types and tool_instances, and migrates the pi-agent tool to a manifest-based definition with a base Ubuntu image. | exp: func:upgrade() → None, call:op.get_bind, call:op.create_table, call:sa.Column, call:sa.UUID, call:sa.String, call:sa.Text, call:sa.JSON, call:sa.Boolean, call:sa.TIMESTAMP, call:sa.func.now, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, call:sa.ForeignKeyConstraint, call:sa.CheckConstraint, call:conn.execute, call:sa.text, call:result.fetchone, call:op.add_column, call:op.create_foreign_key, call:op.drop_constraint, call:op.execute, call:json.dumps, call:str, func:downgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:op.drop_column, call:op.drop_constraint, call:op.drop_table | dep: json, uuid, typing, alembic, sqlalchemy
+- 2026_05_28_drop_tool_configs_and_config_folders.py | Alembic database migration that drops the tool_configs and config_folders tables with conditional existence checks, and provides downgrade to recreate them | exp: func:upgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:op.drop_table, func:downgrade() → None, call:op.create_table, call:sa.Column, call:sa.UUID, call:sa.String, call:sa.Text, call:sa.JSON, call:sa.Boolean, call:sa.TIMESTAMP, call:sa.func.now, call:sa.PrimaryKeyConstraint, call:sa.Integer | dep: typing, alembic, sqlalchemy
+- 2026_05_29_add_notifications_table.py | Creates a notifications table with user-linked, categorized, severity-graded messages supporting read/dismissed states and optimized querying via partial indexes. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.Uuid, call:sa.String, call:sa.Text, call:sa.JSON, call:sa.DateTime, call:sa.func.now, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, call:sa.text, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy
+- 2026_05_29_add_ssh_key_ids_to_tool_instances.py | Alembic database migration that adds a JSON ssh_key_ids column to the tool_instances table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.JSON, func:downgrade() → None, call:op.drop_column | dep: alembic, sqlalchemy
+- 2026_05_29_drop_ssh_key_id_from_config_profiles.py | Alembic database migration that removes the ssh_key_id column from the config_profiles table | exp: func:upgrade() → None, call:op.drop_column, func:downgrade() → None, call:op.add_column, call:sa.Column, call:sa.Uuid, call:sa.ForeignKey | dep: alembic, sqlalchemy
+- 2026_05_29_fix_code_server_bind_addr.py | Alembic database migration that fixes code-server tool type compose templates by replacing deprecated --bind-addr flag with --host flag | exp: func:upgrade() → None, call:op.get_bind, call:conn.execute( sa.text(""" SELECT id, compose_template FROM tool_types WHERE name = 'code-server' AND compose_template LIKE '%--bind-addr%' """) ).fetchall, call:sa.text, call:compose_template.replace( "--bind-addr 0.0.0.0:8443", "--host 0.0.0.0" ).replace, call:print, func:downgrade() → None | dep: typing, alembic, sqlalchemy
+- 2026_05_29_fix_code_server_bind_addr_port.py | Alembic database migration that fixes code-server Docker compose templates by replacing incorrect `--host` flags with proper `--bind-addr 0.0.0.0:PORT` configurations in both database-stored tool type templates and on-disk instance compose files. | exp: func:_fix_tool_type_templates(conn) → None, call:conn.execute( sa.text(""" SELECT id, compose_template, default_port FROM tool_types WHERE name = 'code-server' AND compose_template LIKE '%--host%' """) ).fetchall, call:sa.text, call:compose_template.split, call:len, call:line.lstrip, call:new_lines.append, call:"\n".join, call:print, func:_fix_instance_compose_files(conn) → None, call:conn.execute( sa.text(""" SELECT column_name FROM information_schema.columns WHERE table_name = 'tool_instances' AND column_name = 'compose_path' """) ).fetchone, call:sa.text, call:print, call:conn.execute( sa.text(""" SELECT id, compose_path, tool_type_id FROM tool_instances WHERE compose_path IS NOT NULL """) ).fetchall, call:Path, call:path.exists, call:path.read_text, call:conn.execute( sa.text(""" SELECT default_port FROM tool_types WHERE id = :id """), {"id": tool_type_id}, ).fetchone, call:yaml.safe_load, call:data["services"].values, call:path.write_text, call:yaml.dump, func:upgrade() → None, call:op.get_bind, call:_fix_tool_type_templates, call:_fix_instance_compose_files, func:downgrade() → None | dep: typing, alembic, yaml, pathlib, sqlalchemy
+- 2026_05_29_fix_web_tool_bind_address.py | Alembic database migration that fixes web tool (code-server and jupyter-notebook) compose templates to bind to 0.0.0.0 for network accessibility. | exp: func:_fix_code_server_compose(conn) → None, call:conn.execute( sa.text(""" SELECT id, compose_template, definition_type FROM tool_types WHERE name = 'code-server' """) ).fetchone, call:sa.text, call:compose_template.split, call:enumerate, call:len, call:line.lstrip, call:new_lines.append, call:image_line.lstrip, call:new_lines.index, call:new_lines.insert, call:"\n".join, call:print, func:_fix_jupyter_compose(conn) → None, call:conn.execute( sa.text(""" SELECT id, compose_template, definition_type FROM tool_types WHERE name = 'jupyter-notebook' """) ).fetchone, call:sa.text, call:compose_template.split, call:enumerate, call:new_lines.append, call:len, call:line.lstrip, call:"\n".join, call:print, func:upgrade() → None, call:op.get_bind, call:_fix_code_server_compose, call:_fix_jupyter_compose, func:downgrade() → None | dep: typing, alembic, sqlalchemy
+- 2026_05_29_remove_lsio_command_override.py | Alembic database migration that removes broken command overrides containing --bind-addr or --host from LinuxServer.io (LSIO) code-server Docker Compose templates in both database tool_types records and on-disk instance compose files. | exp: func:upgrade() → None, call:op.get_bind, call:conn.execute( sa.text(""" SELECT id, compose_template FROM tool_types WHERE name = 'code-server' """) ).fetchall, call:sa.text, call:yaml.safe_load, call:data["services"].values, call:svc.get, call:yaml.dump, call:print, call:conn.execute( sa.text(""" SELECT column_name FROM information_schema.columns WHERE table_name = 'tool_instances' AND column_name = 'compose_path' """) ).fetchone, call:conn.execute( sa.text(""" SELECT id, compose_path FROM tool_instances WHERE compose_path IS NOT NULL """) ).fetchall, call:Path, call:path.exists, call:path.read_text, call:path.write_text, func:downgrade() → None | dep: collections.abc, alembic, yaml, pathlib, sqlalchemy
+- 2026_05_29_remove_ssh_keys_mount_from_manifest.py | Alembic database migration that removes the ssh_keys mount from the pi-agent manifest in the tool_definition_manifests table, with downgrade support to restore it. | exp: func:upgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:isinstance, call:json.loads, call:manifest.get, call:len, call:m.get, call:json.dumps, func:downgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:isinstance, call:json.loads, call:manifest.get, call:any, call:m.get, call:mounts.append, call:json.dumps | dep: json, typing, alembic, sqlalchemy
+- 2026_06_01_add_workspaces.py | Alembic database migration that creates a workspaces table with foreign keys to git_repositories and users, adds indexes, and adds a workspace_id column to tool_instances. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.Uuid, call:sa.String, call:sa.ForeignKey, call:sa.DateTime, call:sa.text, call:sa.UniqueConstraint, call:op.create_index, call:op.add_column, func:downgrade() → None, call:op.drop_index, call:op.drop_column, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy
+- 2026_06_13_make_clone_mode_nullable.py | Alembic database migration that makes the `clone_mode` column in the `tool_instances` table nullable to allow NULL values for new rows. | exp: func:upgrade() → None, call:op.alter_column, call:sa.String, func:downgrade() → None, call:op.alter_column, call:sa.String | dep: alembic, sqlalchemy
+- 2026_06_14_104415_add_tool_type_home_directory.py | An Alembic database migration that adds a `home_directory` column to `tool_types` table and updates template strings from `/workspace` to a configurable `/home/user/{{WORKSPACE_NAME}}` path. | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.String, call:op.execute, call:sa.update(tool_types) .where(tool_types.c.compose_template.is_not(None)) .values, call:tool_types.c.compose_template.is_not, call:sa.func.replace, call:sa.update(tool_types) .where(tool_types.c.dockerfile_template.is_not(None)) .values, call:tool_types.c.dockerfile_template.is_not, func:downgrade() → None, call:op.execute, call:sa.update(tool_types) .where(tool_types.c.compose_template.is_not(None)) .values, call:tool_types.c.compose_template.is_not, call:sa.func.replace, call:sa.update(tool_types) .where(tool_types.c.dockerfile_template.is_not(None)) .values, call:tool_types.c.dockerfile_template.is_not, call:op.drop_column | dep: typing, alembic, sqlalchemy.sql, sqlalchemy
+- 2026_06_14_182955_fix_pi_agent_home_directory_mount.py | Alembic database migration that fixes the pi-agent tool definition manifest's home directory mount path from /workspace to ~/{{WORKSPACE_NAME}} with a compatibility symlink and updated startup script. | exp: func:_find_pi_agent_manifest(conn: sa.Connection) → tuple[Union[str, None], Union[dict, None]], call:conn.execute( sa.select(tool_definition_manifests.c.id, tool_definition_manifests.c.manifest) .where(tool_definition_manifests.c.name == "pi-agent") ).fetchone, call:sa.select(tool_definition_manifests.c.id, tool_definition_manifests.c.manifest) .where, call:dict, func:_update_manifest(conn: sa.Connection, manifest_id: str, manifest: dict) → None, call:conn.execute, call:sa.update(tool_definition_manifests) .where(tool_definition_manifests.c.id == manifest_id) .values, func:upgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.get, call:mount.get, call:manifest.setdefault, call:_update_manifest, func:downgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.get, call:mount.get, call:manifest.setdefault, call:_update_manifest | dep: typing, alembic, sqlalchemy.sql, sqlalchemy
+- 2026_06_15_090500_remove_pi_agent_explicit_repo_mount.py | Alembic database migration that removes explicit repo mounts from the pi-agent tool definition manifest and restores them on downgrade | exp: func:_find_pi_agent_manifest(conn: sa.Connection) → tuple[Union[str, None], Union[dict, None]], call:conn.execute( sa.select( tool_definition_manifests.c.id, tool_definition_manifests.c.manifest ).where(tool_definition_manifests.c.name == "pi-agent") ).fetchone, call:sa.select( tool_definition_manifests.c.id, tool_definition_manifests.c.manifest ).where, call:dict, func:_update_manifest(conn: sa.Connection, manifest_id: str, manifest: dict) → None, call:conn.execute, call:sa.update(tool_definition_manifests) .where(tool_definition_manifests.c.id == manifest_id) .values, func:upgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.get, call:mount.get, call:_update_manifest, func:downgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.setdefault, call:any, call:mount.get, call:mounts.append, call:_update_manifest | dep: typing, alembic, sqlalchemy.sql, sqlalchemy
+- 2026_06_19_113000_remove_pi_agent_workspace_symlink.py | Alembic database migration that updates the pi-agent tool definition manifest to remove the /workspace symlink dependency and adjust working directory and startup script accordingly. | exp: func:_find_pi_agent_manifest(conn: sa.Connection) → tuple[str | None, dict | None], call:conn.execute( sa.select( tool_definition_manifests.c.id, tool_definition_manifests.c.manifest ).where(tool_definition_manifests.c.name == "pi-agent") ).fetchone, call:sa.select( tool_definition_manifests.c.id, tool_definition_manifests.c.manifest ).where, call:dict, func:_update_manifest(conn: sa.Connection, manifest_id: str, manifest: dict) → None, call:conn.execute, call:sa.update(tool_definition_manifests) .where(tool_definition_manifests.c.id == manifest_id) .values, func:upgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.setdefault, call:runtime.get, call:_update_manifest, func:downgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.setdefault, call:_update_manifest | dep: collections.abc, alembic, sqlalchemy.sql, sqlalchemy
+- 398082499c30_add_tool_config_fields.py | Alembic database migration that adds configuration fields (port_override, start_command, working_directory, environment_variables, volumes) to the tool_configs table with a port range validation constraint. | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.Integer, call:sa.Text, call:postgresql.JSONB, call:op.create_check_constraint, call:sa.text, func:downgrade() → None, call:op.drop_constraint, call:op.drop_column | dep: alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- 6fc7bfcf199f_merge_remove_is_builtin_and_add_config_.py | Alembic merge migration that combines two parallel migration branches (remove_is_builtin and add_config_profiles) into a single revision history | exp: func:upgrade() → None, func:downgrade() → None | dep: alembic
+- 86cec91fdb00_merge_profile_resolver_and_workspaces_.py | Merges two Alembic migration branches (profile resolver and workspaces) into a single migration head | exp: func:upgrade() → None, func:downgrade() → None | dep: alembic
+- 8c6d1dbd4798_remove_pi_config_and_state_mounts_from_.py | Alembic database migration that removes or restores pi_state and pi_config mounts from a JSON manifest stored in the tool_definition_manifests table for the 'pi-agent' tool. | exp: func:_load_manifest(manifest_json), call:isinstance, call:json.loads, func:upgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:_load_manifest, call:manifest.get, call:len, call:m.get, call:json.dumps, func:downgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:_load_manifest, call:manifest.get, call:m.get, call:mounts.append, call:json.dumps | dep: json, alembic, sqlalchemy
+- 8ed7dd80973d_create_config_folders_table.py | Alembic database migration that creates a config_folders table with UUID primary key, user foreign key, JSONB fields for files and project overrides, and supporting indexes/constraints | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.text, call:sa.ForeignKey, call:sa.String, call:sa.Text, call:postgresql.JSONB, call:sa.Boolean, call:sa.DateTime, call:sa.UniqueConstraint, call:op.create_index, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: alembic, sqlalchemy.dialects, sqlalchemy, postgresql dialect
+- af8512103d67_add_tool_type_fields.py | Alembic database migration that adds columns (definition_type, dockerfile_template, build_context, readiness_probe) and a check constraint to the tool_types table. | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.String, call:sa.Text, call:postgresql.JSONB, call:op.create_check_constraint, call:sa.text, func:downgrade() → None, call:op.drop_constraint, call:op.drop_column | dep: alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
+- f3d2dc90ba3a_merge_single_interface_and_clone_mode.py | Alembic database migration that merges two previous migrations (single_interface and clone_mode) into a single revision point | exp: func:upgrade() → None, func:downgrade() → None | dep: typing, alembic
+- fc8f1a20cbf6_merge_home_directory_and_pi_agent_mount_.py | Alembic database migration that merges two branch heads (home directory and pi agent mount cleanup) into a single revision point | exp: func:upgrade() → None, func:downgrade() → None | dep: alembic
+## arch
+Linear migration history with occasional branch/merge patterns (using merge heads), sequential numbered and timestamped revision files, each containing declarative schema changes (CREATE TABLE/ALTER TABLE/DROP TABLE) with idempotent guards, downgrade paths, and occasional data migrations; supports PostgreSQL and SQLite dialects.
+## tags
+column, table, call:op.drop, downgrade, upgrade, alembic, key, call:sa.text
+## symbols
+- upgrade
+- downgrade
+- _table_exists
+- _column_exists
+- _index_exists
+- _foreign_key_exists
+- _foreign_key_names_for_column
+- _get_dialect
+## workflows
+- change versions behavior
+  read: 0001_initial_schema.py, 0002_refresh_tokens.py, 0003_user_configs.py
+- change versions CLI
+  read: 2026_05_24_220141_add_startup_command.py, 2026_05_29_remove_lsio_command_override.py
+- change versions config
+  read: 0003_user_configs.py, 0009_tool_configs.py, 0013_add_config_profiles.py
+- explore versions subdirectories
+  index: apps/api/alembic/versions/.ruff_cache/.pi-map.index.md
+## dirty
+-

apps/api/alembic/versions/0013_add_config_profiles.py

@@ -0,0 +1,204 @@
+"""add config profiles, includes, mounts, and tool instance profile selection
+
+Revision ID: 0013_add_config_profiles
+Revises: 0012_default_port_req
+Create Date: 2026-05-24 12:00:00.000000
+
+"""
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0013_add_config_profiles"
+down_revision: str | None = "0012_default_port_req"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def _table_exists(table_name: str) -> bool:
+    return sa.inspect(op.get_bind()).has_table(table_name)
+
+
+def _column_exists(table_name: str, column_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return column_name in {
+        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
+    }
+
+
+def _index_exists(table_name: str, index_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return index_name in {
+        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
+    }
+
+
+def _foreign_key_exists(
+    table_name: str,
+    constrained_columns: list[str],
+    referred_table: str,
+) -> bool:
+    if not _table_exists(table_name):
+        return False
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if (
+            foreign_key.get("constrained_columns") == constrained_columns
+            and foreign_key.get("referred_table") == referred_table
+        ):
+            return True
+    return False
+
+
+def upgrade() -> None:
+    # Earlier branches may already have created config_profiles. Keep this
+    # migration defensive so databases can converge onto the current graph.
+    if not _table_exists("config_profiles"):
+        op.create_table(
+            "config_profiles",
+            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("user_id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("name", sa.String(length=255), nullable=False),
+            sa.Column("description", sa.Text(), nullable=True),
+            sa.Column(
+                "created_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.Column(
+                "updated_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.ForeignKeyConstraint(["user_id"], ["users.id"], ondelete="CASCADE"),
+            sa.PrimaryKeyConstraint("id"),
+            sa.UniqueConstraint(
+                "user_id", "name", name="uq_config_profiles_user_name"
+            ),
+        )
+    if not _index_exists("config_profiles", "idx_config_profiles_user"):
+        op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
+
+    if not _table_exists("config_includes"):
+        op.create_table(
+            "config_includes",
+            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column(
+                "included_profile_id", postgresql.UUID(as_uuid=True), nullable=False
+            ),
+            sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+            sa.Column(
+                "created_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.Column(
+                "updated_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.ForeignKeyConstraint(
+                ["profile_id"], ["config_profiles.id"], ondelete="CASCADE"
+            ),
+            sa.ForeignKeyConstraint(
+                ["included_profile_id"],
+                ["config_profiles.id"],
+                ondelete="CASCADE",
+            ),
+            sa.PrimaryKeyConstraint("id"),
+            sa.UniqueConstraint(
+                "profile_id", "included_profile_id", name="uq_config_includes_pair"
+            ),
+        )
+    if not _index_exists("config_includes", "idx_config_includes_profile"):
+        op.create_index("idx_config_includes_profile", "config_includes", ["profile_id"])
+    if not _index_exists("config_includes", "idx_config_includes_included"):
+        op.create_index(
+            "idx_config_includes_included", "config_includes", ["included_profile_id"]
+        )
+
+    if not _table_exists("config_mounts"):
+        op.create_table(
+            "config_mounts",
+            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+            sa.Column("mount_path", sa.String(length=1024), nullable=False),
+            sa.Column("content", sa.Text(), nullable=True),
+            sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+            sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+            sa.Column(
+                "created_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.Column(
+                "updated_at",
+                sa.DateTime(timezone=True),
+                server_default=sa.text("NOW()"),
+                nullable=False,
+            ),
+            sa.ForeignKeyConstraint(
+                ["profile_id"], ["config_profiles.id"], ondelete="CASCADE"
+            ),
+            sa.ForeignKeyConstraint(
+                ["source_profile_id"], ["config_profiles.id"], ondelete="SET NULL"
+            ),
+            sa.PrimaryKeyConstraint("id"),
+        )
+    if not _index_exists("config_mounts", "idx_config_mounts_profile"):
+        op.create_index("idx_config_mounts_profile", "config_mounts", ["profile_id"])
+
+    if not _column_exists("tool_instances", "selected_profile_id"):
+        op.add_column(
+            "tool_instances",
+            sa.Column("selected_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _foreign_key_exists(
+        "tool_instances", ["selected_profile_id"], "config_profiles"
+    ):
+        op.create_foreign_key(
+            "fk_tool_instances_selected_profile",
+            "tool_instances",
+            "config_profiles",
+            ["selected_profile_id"],
+            ["id"],
+            ondelete="SET NULL",
+        )
+    if not _index_exists("tool_instances", "idx_tool_instances_selected_profile"):
+        op.create_index(
+            "idx_tool_instances_selected_profile",
+            "tool_instances",
+            ["selected_profile_id"],
+        )
+
+
+def downgrade() -> None:
+    # Remove selected_profile_id from tool_instances
+    op.drop_index("idx_tool_instances_selected_profile", table_name="tool_instances")
+    op.drop_constraint(
+        "fk_tool_instances_selected_profile", "tool_instances", type_="foreignkey"
+    )
+    op.drop_column("tool_instances", "selected_profile_id")
+
+    # Drop config_mounts
+    op.drop_index("idx_config_mounts_profile", table_name="config_mounts")
+    op.drop_table("config_mounts")
+
+    # Drop config_includes
+    op.drop_index("idx_config_includes_included", table_name="config_includes")
+    op.drop_index("idx_config_includes_profile", table_name="config_includes")
+    op.drop_table("config_includes")
+
+    # Drop config_profiles
+    op.drop_index("idx_config_profiles_user", table_name="config_profiles")
+    op.drop_table("config_profiles")

apps/api/alembic/versions/0014_add_profile_resolver_fields.py

@@ -0,0 +1,180 @@
+"""add profile resolver fields to config profiles and mounts
+
+Revision ID: 0014_add_profile_resolver_fields
+Revises: 0013_add_config_profiles
+Create Date: 2026-05-24 14:00:00.000000
+
+"""
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = "0014_add_profile_resolver_fields"
+down_revision: str | None = "0013_add_config_profiles"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def _table_exists(table_name: str) -> bool:
+    return sa.inspect(op.get_bind()).has_table(table_name)
+
+
+def _column_exists(table_name: str, column_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return column_name in {
+        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
+    }
+
+
+def _index_exists(table_name: str, index_name: str) -> bool:
+    if not _table_exists(table_name):
+        return False
+    return index_name in {
+        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
+    }
+
+
+def _foreign_key_exists(
+    table_name: str,
+    constrained_columns: list[str],
+    referred_table: str,
+) -> bool:
+    if not _table_exists(table_name):
+        return False
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if (
+            foreign_key.get("constrained_columns") == constrained_columns
+            and foreign_key.get("referred_table") == referred_table
+        ):
+            return True
+    return False
+
+
+def _foreign_key_names_for_column(table_name: str, column_name: str) -> list[str]:
+    if not _table_exists(table_name):
+        return []
+    names: list[str] = []
+    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
+        if column_name in foreign_key.get("constrained_columns", []):
+            name = foreign_key.get("name")
+            if name:
+                names.append(name)
+    return names
+
+
+def upgrade() -> None:
+    if not _column_exists("config_profiles", "project_id"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _column_exists("config_profiles", "tool_type_id"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=True),
+        )
+    if not _column_exists("config_profiles", "environment_variables"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("environment_variables", sa.JSON(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "start_command"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("start_command", sa.Text(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "working_directory"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("working_directory", sa.Text(), nullable=True),
+        )
+    if not _column_exists("config_profiles", "port"):
+        op.add_column("config_profiles", sa.Column("port", sa.Integer(), nullable=True))
+    if not _column_exists("config_profiles", "is_default"):
+        op.add_column(
+            "config_profiles",
+            sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
+        )
+
+    if not _foreign_key_exists("config_profiles", ["project_id"], "projects"):
+        op.create_foreign_key(
+            "fk_config_profiles_project",
+            "config_profiles",
+            "projects",
+            ["project_id"],
+            ["id"],
+            ondelete="CASCADE",
+        )
+    if not _foreign_key_exists("config_profiles", ["tool_type_id"], "tool_types"):
+        op.create_foreign_key(
+            "fk_config_profiles_tool_type",
+            "config_profiles",
+            "tool_types",
+            ["tool_type_id"],
+            ["id"],
+            ondelete="CASCADE",
+        )
+
+    if not _index_exists("config_profiles", "idx_config_profiles_project"):
+        op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
+    if not _index_exists("config_profiles", "idx_config_profiles_tool_type"):
+        op.create_index(
+            "idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"]
+        )
+
+    if _column_exists("config_mounts", "mount_path") and not _column_exists(
+        "config_mounts", "target_path"
+    ):
+        op.alter_column("config_mounts", "mount_path", new_column_name="target_path")
+    if not _column_exists("config_mounts", "mode"):
+        op.add_column(
+            "config_mounts",
+            sa.Column("mode", sa.String(length=10), nullable=False, server_default="rw"),
+        )
+    if not _column_exists("config_mounts", "files"):
+        op.add_column(
+            "config_mounts",
+            sa.Column("files", sa.JSON(), nullable=True),
+        )
+    for constraint_name in _foreign_key_names_for_column(
+        "config_mounts", "source_profile_id"
+    ):
+        op.drop_constraint(constraint_name, "config_mounts", type_="foreignkey")
+    if _column_exists("config_mounts", "content"):
+        op.drop_column("config_mounts", "content")
+    if _column_exists("config_mounts", "source_profile_id"):
+        op.drop_column("config_mounts", "source_profile_id")
+
+
+def downgrade() -> None:
+    # Restore config_mounts
+    op.add_column(
+        "config_mounts",
+        sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.add_column(
+        "config_mounts",
+        sa.Column("content", sa.Text(), nullable=True),
+    )
+    op.drop_column("config_mounts", "files")
+    op.drop_column("config_mounts", "mode")
+    op.alter_column("config_mounts", "target_path", new_column_name="mount_path")
+
+    # Restore config_profiles
+    op.drop_index("idx_config_profiles_tool_type", table_name="config_profiles")
+    op.drop_index("idx_config_profiles_project", table_name="config_profiles")
+    op.drop_constraint(
+        "fk_config_profiles_tool_type", "config_profiles", type_="foreignkey"
+    )
+    op.drop_constraint("fk_config_profiles_project", "config_profiles", type_="foreignkey")
+    op.drop_column("config_profiles", "is_default")
+    op.drop_column("config_profiles", "port")
+    op.drop_column("config_profiles", "working_directory")
+    op.drop_column("config_profiles", "start_command")
+    op.drop_column("config_profiles", "environment_variables")
+    op.drop_column("config_profiles", "tool_type_id")
+    op.drop_column("config_profiles", "project_id")

apps/api/alembic/versions/069d3da4dc9b_add_ssh_key_id_to_config_profiles.py

@@ -0,0 +1,32 @@
+"""add_ssh_key_id_to_config_profiles
+
+Revision ID: 069d3da4dc9b
+Revises: 2026_05_29_add_notifications_table
+Create Date: 2026-05-29 12:30:16.580532
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "069d3da4dc9b"
+down_revision = "2026_05_29_add_notifications_table"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "config_profiles",
+        sa.Column(
+            "ssh_key_id",
+            sa.Uuid(),
+            sa.ForeignKey("ssh_keys.id", ondelete="SET NULL"),
+            nullable=True,
+        ),
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("config_profiles", "ssh_key_id")

apps/api/alembic/versions/20260527160017_add_pi_agent_tool_type.py

@@ -104,11 +104,11 @@ RUN git config --global init.defaultBranch main \\
     && git config --global user.name "Developer"
 
 # Create default tmux config
-RUN echo 'set -g mouse on\\nset -g default-terminal "screen-256color"' > /home/user/.tmux.conf
+RUN printf '%s\\n' 'set -g mouse on' 'set -g default-terminal "screen-256color"' > /home/user/.tmux.conf
 
 # Create default ranger config
 RUN mkdir -p /home/user/.config/ranger \\
-    && echo 'set preview_files true\\nset use_preview_script true' > /home/user/.config/ranger/rc.conf
+    && printf '%s\\n' 'set preview_files true' 'set use_preview_script true' > /home/user/.config/ranger/rc.conf
 
 # Set up Pi config directory
 RUN mkdir -p /home/user/.pi/agent

apps/api/alembic/versions/2026_05_28_add_monitoring_tables.py

@@ -0,0 +1,122 @@
+"""add monitoring tables
+
+Revision ID: 2026_05_28_add_monitoring_tables
+Revises: 2026_05_28_drop_tool_configs_and_config_folders
+Create Date: 2026-05-28
+
+"""
+
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_28_add_monitoring_tables"
+down_revision: str | None = "2026_05_28_drop_tool_configs_and_config_folders"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "instance_events",
+        sa.Column("id", sa.Uuid(), nullable=False),
+        sa.Column(
+            "instance_id",
+            sa.Uuid(),
+            nullable=False,
+        ),
+        sa.Column("event_type", sa.String(length=50), nullable=False),
+        sa.Column("status", sa.String(length=50), nullable=True),
+        sa.Column("message", sa.Text(), nullable=True),
+        sa.Column("created_by", sa.Uuid(), nullable=True),
+        sa.Column(
+            "metadata",
+            sa.JSON(),
+            nullable=False,
+            server_default="{}",
+        ),
+        sa.Column(
+            "created_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.func.now(),
+            nullable=False,
+        ),
+        sa.ForeignKeyConstraint(
+            ["instance_id"],
+            ["tool_instances.id"],
+            ondelete="CASCADE",
+        ),
+        sa.ForeignKeyConstraint(
+            ["created_by"],
+            ["users.id"],
+            ondelete="SET NULL",
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        "idx_instance_events_instance_id",
+        "instance_events",
+        ["instance_id"],
+    )
+    op.create_index(
+        "idx_instance_events_created_at",
+        "instance_events",
+        ["created_at"],
+        postgresql_using="btree",
+    )
+    op.create_index(
+        "idx_instance_events_event_type",
+        "instance_events",
+        ["event_type"],
+    )
+
+    op.create_table(
+        "health_checks",
+        sa.Column("id", sa.Uuid(), nullable=False),
+        sa.Column(
+            "instance_id",
+            sa.Uuid(),
+            nullable=False,
+        ),
+        sa.Column("container_status", sa.String(length=50), nullable=True),
+        sa.Column("container_healthy", sa.Boolean(), nullable=True),
+        sa.Column("tunnel_healthy", sa.Boolean(), nullable=True),
+        sa.Column("exit_code", sa.Integer(), nullable=True),
+        sa.Column("probe_status", sa.String(length=50), nullable=True),
+        sa.Column("probe_output", sa.Text(), nullable=True),
+        sa.Column(
+            "checked_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.func.now(),
+            nullable=False,
+        ),
+        sa.ForeignKeyConstraint(
+            ["instance_id"],
+            ["tool_instances.id"],
+            ondelete="CASCADE",
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        "idx_health_checks_instance_id",
+        "health_checks",
+        ["instance_id"],
+    )
+    op.create_index(
+        "idx_health_checks_checked_at",
+        "health_checks",
+        ["checked_at"],
+        postgresql_using="btree",
+    )
+
+
+def downgrade() -> None:
+    op.drop_index("idx_health_checks_checked_at", table_name="health_checks")
+    op.drop_index("idx_health_checks_instance_id", table_name="health_checks")
+    op.drop_table("health_checks")
+    op.drop_index("idx_instance_events_event_type", table_name="instance_events")
+    op.drop_index("idx_instance_events_created_at", table_name="instance_events")
+    op.drop_index("idx_instance_events_instance_id", table_name="instance_events")
+    op.drop_table("instance_events")

apps/api/alembic/versions/2026_05_28_add_terminal_sessions_table.py

@@ -0,0 +1,61 @@
+"""add terminal_sessions table
+
+Revision ID: 2026_05_28_add_terminal_sessions
+Revises: 20260527_160017_add_pi_agent
+Create Date: 2026-05-28
+
+"""
+
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_28_add_terminal_sessions"
+down_revision: str | None = "2026_05_28_add_tool_definition_manifests"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "terminal_sessions",
+        sa.Column("id", sa.UUID(), nullable=False),
+        sa.Column("instance_id", sa.UUID(), nullable=False),
+        sa.Column("name", sa.String(length=255), nullable=True),
+        sa.Column("status", sa.String(length=50), nullable=False),
+        sa.Column("last_activity_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("closed_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "created_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.Column(
+            "updated_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            onupdate=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.ForeignKeyConstraint(
+            ["instance_id"], ["tool_instances.id"], ondelete="CASCADE"
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        op.f("ix_terminal_sessions_instance_id"),
+        "terminal_sessions",
+        ["instance_id"],
+        unique=False,
+    )
+
+
+def downgrade() -> None:
+    op.drop_index(
+        op.f("ix_terminal_sessions_instance_id"),
+        table_name="terminal_sessions",
+    )
+    op.drop_table("terminal_sessions")

apps/api/alembic/versions/2026_05_28_add_tool_definition_manifests.py

@@ -232,28 +232,6 @@ def upgrade() -> None:
                             "writable": True,
                             "owner": "user",
                         },
-                        {
-                            "name": "ssh_keys",
-                            "target": "/home/user/.ssh",
-                            "source_type": "ssh_key",
-                            "mode": "0700",
-                            "file_mode": "0600",
-                            "readonly": True,
-                        },
-                        {
-                            "name": "pi_state",
-                            "target": "/tmp/.pi/agents",
-                            "source_type": "instance",
-                            "writable": True,
-                        },
-                        {
-                            "name": "pi_config",
-                            "target": "/home/user/.pi",
-                            "source_type": "git_mount",
-                            "git_mount_ref": "dotfiles",
-                            "writable": True,
-                            "owner": "user",
-                        },
                     ],
                     "runtime": {
                         "command": ["/bin/bash"],
@@ -330,10 +308,10 @@ RUN git config --global init.defaultBranch main \\
     && git config --global user.email "dev@headquarter.local" \\
     && git config --global user.name "Developer"
 
-RUN echo 'set -g mouse on\\nset -g default-terminal "screen-256color"' > /home/user/.tmux.conf
+RUN printf '%s\\n' 'set -g mouse on' 'set -g default-terminal "screen-256color"' > /home/user/.tmux.conf
 
 RUN mkdir -p /home/user/.config/ranger \\
-    && echo 'set preview_files true\\nset use_preview_script true' > /home/user/.config/ranger/rc.conf
+    && printf '%s\\n' 'set preview_files true' 'set use_preview_script true' > /home/user/.config/ranger/rc.conf
 
 RUN mkdir -p /home/user/.pi/agent
 

apps/api/alembic/versions/2026_05_28_drop_tool_configs_and_config_folders.py

@@ -0,0 +1,89 @@
+"""drop tool_configs and config_folders tables
+
+Revision ID: 2026_05_28_drop_tool_configs_and_config_folders
+Revises: 2026_05_28_add_tool_definition_manifests
+Create Date: 2026-05-28
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_28_drop_tool_configs_and_config_folders"
+down_revision: Union[str, None] = "2026_05_28_add_terminal_sessions"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+
+    # Drop tool_configs table if it exists
+    result = conn.execute(
+        sa.text("""
+            SELECT table_name FROM information_schema.tables
+            WHERE table_name = 'tool_configs'
+        """)
+    )
+    if result.fetchone():
+        op.drop_table("tool_configs")
+
+    # Drop config_folders table if it exists
+    result = conn.execute(
+        sa.text("""
+            SELECT table_name FROM information_schema.tables
+            WHERE table_name = 'config_folders'
+        """)
+    )
+    if result.fetchone():
+        op.drop_table("config_folders")
+
+
+def downgrade() -> None:
+    # Recreate config_folders table
+    op.create_table(
+        "config_folders",
+        sa.Column("id", sa.UUID(), nullable=False),
+        sa.Column("user_id", sa.UUID(), nullable=False),
+        sa.Column("name", sa.String(255), nullable=False),
+        sa.Column("description", sa.Text(), nullable=True),
+        sa.Column("mount_path", sa.String(1024), nullable=False),
+        sa.Column("files", sa.JSON(), default=dict, nullable=False),
+        sa.Column("project_overrides", sa.JSON(), default=dict, nullable=True),
+        sa.Column("is_active", sa.Boolean(), default=True, nullable=False),
+        sa.Column(
+            "created_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
+        ),
+        sa.Column(
+            "updated_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+
+    # Recreate tool_configs table
+    op.create_table(
+        "tool_configs",
+        sa.Column("id", sa.UUID(), nullable=False),
+        sa.Column("user_id", sa.UUID(), nullable=False),
+        sa.Column("tool_type_id", sa.UUID(), nullable=False),
+        sa.Column("project_id", sa.UUID(), nullable=True),
+        sa.Column("key", sa.String(255), nullable=False),
+        sa.Column("value", sa.Text(), nullable=False),
+        sa.Column("config_type", sa.String(20), default="env", nullable=False),
+        sa.Column("file_path", sa.String(1024), nullable=True),
+        sa.Column("port_override", sa.Integer(), nullable=True),
+        sa.Column("start_command", sa.Text(), nullable=True),
+        sa.Column("working_directory", sa.Text(), nullable=True),
+        sa.Column("environment_variables", sa.JSON(), default=dict, nullable=True),
+        sa.Column("volumes", sa.JSON(), default=list, nullable=True),
+        sa.Column(
+            "created_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
+        ),
+        sa.Column(
+            "updated_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )

apps/api/alembic/versions/2026_05_29_add_notifications_table.py

@@ -0,0 +1,69 @@
+"""add notifications table
+
+Revision ID: 2026_05_29_add_notifications_table
+Revises: 2026_05_28_add_monitoring_tables
+Create Date: 2026-05-29
+
+"""
+
+from collections.abc import Sequence
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_add_notifications_table"
+down_revision: str | None = "2026_05_28_add_monitoring_tables"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "notifications",
+        sa.Column("id", sa.Uuid(), nullable=False),
+        sa.Column("user_id", sa.Uuid(), nullable=False),
+        sa.Column("category", sa.String(length=32), nullable=False),
+        sa.Column("severity", sa.String(length=16), nullable=False),
+        sa.Column("title", sa.String(length=255), nullable=False),
+        sa.Column("message", sa.Text(), nullable=True),
+        sa.Column("source_type", sa.String(length=64), nullable=True),
+        sa.Column("source_id", sa.Uuid(), nullable=True),
+        sa.Column(
+            "metadata",
+            sa.JSON(),
+            nullable=False,
+            server_default="{}",
+        ),
+        sa.Column("read_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("dismissed_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "created_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.func.now(),
+            nullable=False,
+        ),
+        sa.ForeignKeyConstraint(
+            ["user_id"],
+            ["users.id"],
+            ondelete="CASCADE",
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        "idx_notifications_user_created_at",
+        "notifications",
+        ["user_id", sa.text("created_at DESC")],
+    )
+    op.create_index(
+        "idx_notifications_user_unread",
+        "notifications",
+        ["user_id", "read_at"],
+        postgresql_where=sa.text("read_at IS NULL"),
+    )
+
+
+def downgrade() -> None:
+    op.drop_index("idx_notifications_user_unread", table_name="notifications")
+    op.drop_index("idx_notifications_user_created_at", table_name="notifications")
+    op.drop_table("notifications")

apps/api/alembic/versions/2026_05_29_add_ssh_key_ids_to_tool_instances.py

@@ -0,0 +1,27 @@
+"""add_ssh_key_ids_to_tool_instances
+
+Revision ID: 2026_05_29_add_ssh_key_ids_to_tool_instances
+Revises: 2026_05_29_drop_ssh_key_id_from_config_profiles
+Create Date: 2026-05-29 12:46:00.000000
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "2026_05_29_add_ssh_key_ids_to_tool_instances"
+down_revision = "2026_05_29_drop_ssh_key_id_from_config_profiles"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.add_column(
+        "tool_instances",
+        sa.Column("ssh_key_ids", sa.JSON(), nullable=True),
+    )
+
+
+def downgrade() -> None:
+    op.drop_column("tool_instances", "ssh_key_ids")

apps/api/alembic/versions/2026_05_29_drop_ssh_key_id_from_config_profiles.py

@@ -0,0 +1,32 @@
+"""drop_ssh_key_id_from_config_profiles
+
+Revision ID: 2026_05_29_drop_ssh_key_id_from_config_profiles
+Revises: 069d3da4dc9b
+Create Date: 2026-05-29 12:45:00.000000
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "2026_05_29_drop_ssh_key_id_from_config_profiles"
+down_revision = "069d3da4dc9b"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.drop_column("config_profiles", "ssh_key_id")
+
+
+def downgrade() -> None:
+    op.add_column(
+        "config_profiles",
+        sa.Column(
+            "ssh_key_id",
+            sa.Uuid(),
+            sa.ForeignKey("ssh_keys.id", ondelete="SET NULL"),
+            nullable=True,
+        ),
+    )

apps/api/alembic/versions/2026_05_29_fix_code_server_bind_addr.py

@@ -0,0 +1,54 @@
+"""fix code-server bind-addr to host in DB template
+
+Revision ID: 2026_05_29_fix_code_server_bind_addr
+Revises: 2026_05_29_fix_web_tool_bind_address
+Create Date: 2026-05-29 15:00:00.000000
+
+"""
+
+from typing import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_fix_code_server_bind_addr"
+down_revision: str | None = "2026_05_29_fix_web_tool_bind_address"
+branch_labels: Sequence[str] | None = None
+depends_on: Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+
+    # Find code-server tool types with broken --bind-addr in compose template
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template
+            FROM tool_types
+            WHERE name = 'code-server'
+            AND compose_template LIKE '%--bind-addr%'
+        """)
+    ).fetchall()
+
+    for tool_id, compose_template in result:
+        updated = compose_template.replace(
+            "--bind-addr 0.0.0.0:8443", "--host 0.0.0.0"
+        ).replace("--bind-addr", "--host 0.0.0.0")
+
+        conn.execute(
+            sa.text("""
+                UPDATE tool_types
+                SET compose_template = :compose_template
+                WHERE id = :id
+            """),
+            {"compose_template": updated, "id": tool_id},
+        )
+
+        print(
+            f"Fixed code-server template ({tool_id}): replaced --bind-addr with --host"
+        )
+
+
+def downgrade() -> None:
+    pass

apps/api/alembic/versions/2026_05_29_fix_code_server_bind_addr_port.py

@@ -0,0 +1,148 @@
+"""Fix code-server bind address to include port
+
+Revision ID: 2026_05_29_fix_code_server_bind_addr_port
+Revises: 2026_05_29_remove_lsio_command_override
+Create Date: 2026-05-29 18:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+import yaml
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_fix_code_server_bind_addr_port"
+down_revision: Union[str, None] = "2026_05_29_remove_lsio_command_override"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def _fix_tool_type_templates(conn) -> None:
+    """Fix code-server tool type templates with broken --host override."""
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template, default_port
+            FROM tool_types
+            WHERE name = 'code-server'
+            AND compose_template LIKE '%--host%'
+        """)
+    ).fetchall()
+
+    for tool_id, compose_template, default_port in result:
+        port = default_port or 8443
+        expected = f"--bind-addr 0.0.0.0:{port}"
+
+        # Replace any line containing --host with the correct bind-addr
+        lines = compose_template.split("\n")
+        new_lines = []
+        modified = False
+        for line in lines:
+            if "command:" in line and "--host" in line:
+                indent = line[: len(line) - len(line.lstrip())]
+                new_lines.append(f"{indent}command: {expected}")
+                modified = True
+            else:
+                new_lines.append(line)
+
+        if not modified:
+            continue
+
+        updated = "\n".join(new_lines)
+        conn.execute(
+            sa.text("""
+                UPDATE tool_types
+                SET compose_template = :compose_template
+                WHERE id = :id
+            """),
+            {"compose_template": updated, "id": tool_id},
+        )
+        print(f"Fixed code-server template ({tool_id}): replaced --host with {expected}")
+
+
+def _fix_instance_compose_files(conn) -> None:
+    """Fix existing instance compose files on disk with broken --host override."""
+    from pathlib import Path
+
+    # Use information_schema to check if compose_path column exists
+    col_result = conn.execute(
+        sa.text("""
+            SELECT column_name
+            FROM information_schema.columns
+            WHERE table_name = 'tool_instances'
+            AND column_name = 'compose_path'
+        """)
+    ).fetchone()
+
+    if not col_result:
+        print("compose_path column not found, skipping instance file fixes")
+        return
+
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_path, tool_type_id
+            FROM tool_instances
+            WHERE compose_path IS NOT NULL
+        """)
+    ).fetchall()
+
+    for instance_id, compose_path, tool_type_id in result:
+        path = Path(compose_path)
+        if not path.exists():
+            continue
+
+        try:
+            content = path.read_text()
+        except Exception:
+            continue
+
+        if "--host" not in content:
+            continue
+
+        # Get default_port from tool_type
+        port_result = conn.execute(
+            sa.text("""
+                SELECT default_port FROM tool_types WHERE id = :id
+            """),
+            {"id": tool_type_id},
+        ).fetchone()
+        port = port_result[0] if port_result and port_result[0] else 8443
+        expected = f"--bind-addr 0.0.0.0:{port}"
+
+        try:
+            data = yaml.safe_load(content)
+        except Exception:
+            continue
+
+        if not data or "services" not in data:
+            continue
+
+        modified = False
+        for svc in data["services"].values():
+            if "command" in svc:
+                cmd = svc["command"]
+                if "--host" in cmd:
+                    svc["command"] = expected
+                    modified = True
+
+        if not modified:
+            continue
+
+        try:
+            path.write_text(yaml.dump(data, default_flow_style=False))
+            print(
+                f"Fixed code-server instance compose ({instance_id}): "
+                f"replaced --host with {expected}"
+            )
+        except Exception as exc:
+            print(f"Failed to fix instance {instance_id}: {exc}")
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+    _fix_tool_type_templates(conn)
+    _fix_instance_compose_files(conn)
+
+
+def downgrade() -> None:
+    pass

apps/api/alembic/versions/2026_05_29_fix_web_tool_bind_address.py

@@ -0,0 +1,140 @@
+"""fix web tool bind address to 0.0.0.0
+
+Revision ID: 2026_05_29_fix_web_tool_bind_address
+Revises: 2026_05_29_remove_ssh_keys_mount_from_manifest
+Create Date: 2026-05-29 14:00:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_fix_web_tool_bind_address"
+down_revision: Union[str, None] = "2026_05_29_remove_ssh_keys_mount_from_manifest"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def _fix_code_server_compose(conn) -> None:
+    """Update code-server compose template to bind to 0.0.0.0."""
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template, definition_type
+            FROM tool_types
+            WHERE name = 'code-server'
+        """)
+    ).fetchone()
+
+    if result is None:
+        return
+
+    tool_id, compose_template, definition_type = result
+
+    if definition_type != "compose" or not compose_template:
+        return
+
+    # Fix or add command to bind to 0.0.0.0
+    lines = compose_template.split("\n")
+    new_lines = []
+    image_line_idx = -1
+    command_fixed = False
+    for i, line in enumerate(lines):
+        # Replace broken --bind-addr with correct --host
+        if "command:" in line and "--bind-addr" in line:
+            indent = line[: len(line) - len(line.lstrip())]
+            new_lines.append(f"{indent}command: --host 0.0.0.0")
+            command_fixed = True
+            continue
+        new_lines.append(line)
+        if "image:" in line and image_line_idx == -1:
+            image_line_idx = i
+
+    # If no command line exists, insert one after image
+    if not command_fixed and image_line_idx != -1:
+        image_line = lines[image_line_idx]
+        indent = image_line[: len(image_line) - len(image_line.lstrip())]
+        # Insert after the image line in new_lines
+        insert_idx = new_lines.index(image_line) + 1
+        new_lines.insert(insert_idx, f"{indent}command: --host 0.0.0.0")
+        command_fixed = True
+
+    if not command_fixed:
+        return
+
+    updated_compose = "\n".join(new_lines)
+
+    conn.execute(
+        sa.text("""
+            UPDATE tool_types
+            SET compose_template = :compose_template
+            WHERE id = :id
+        """),
+        {"compose_template": updated_compose, "id": tool_id},
+    )
+
+    print(f"Updated code-server tool type ({tool_id}) to bind to 0.0.0.0")
+
+
+def _fix_jupyter_compose(conn) -> None:
+    """Update jupyter-notebook compose template to bind to 0.0.0.0."""
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template, definition_type
+            FROM tool_types
+            WHERE name = 'jupyter-notebook'
+        """)
+    ).fetchone()
+
+    if result is None:
+        return
+
+    tool_id, compose_template, definition_type = result
+
+    if definition_type != "compose" or not compose_template:
+        return
+
+    if "command:" in compose_template:
+        return
+
+    lines = compose_template.split("\n")
+    new_lines = []
+    image_line_idx = -1
+    for i, line in enumerate(lines):
+        new_lines.append(line)
+        if "image:" in line and image_line_idx == -1:
+            image_line_idx = i
+            indent = line[: len(line) - len(line.lstrip())]
+            # Jupyter needs --ip=0.0.0.0 to bind to all interfaces
+            new_lines.append(
+                f"{indent}command: start-notebook.sh --ip=0.0.0.0 --port=8888 --no-browser"
+            )
+
+    if image_line_idx == -1:
+        return
+
+    updated_compose = "\n".join(new_lines)
+
+    conn.execute(
+        sa.text("""
+            UPDATE tool_types
+            SET compose_template = :compose_template
+            WHERE id = :id
+        """),
+        {"compose_template": updated_compose, "id": tool_id},
+    )
+
+    print(f"Updated jupyter-notebook tool type ({tool_id}) to bind to 0.0.0.0:8888")
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+    _fix_code_server_compose(conn)
+    _fix_jupyter_compose(conn)
+
+
+def downgrade() -> None:
+    # Cannot safely downgrade without knowing the original compose_template
+    pass

apps/api/alembic/versions/2026_05_29_remove_lsio_command_override.py

@@ -0,0 +1,121 @@
+"""Remove broken command override from LSIO code-server templates
+
+Revision ID: 2026_05_29_remove_lsio_command_override
+Revises: 2026_05_29_fix_code_server_bind_addr
+Create Date: 2026-05-29 15:05:00.000000
+
+"""
+
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_remove_lsio_command_override"
+down_revision: str | None = "2026_05_29_fix_code_server_bind_addr"
+branch_labels: Sequence[str] | None = None
+depends_on: Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+
+    # Fix tool_types templates in DB
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template
+            FROM tool_types
+            WHERE name = 'code-server'
+        """)
+    ).fetchall()
+
+    import yaml
+    from pathlib import Path
+
+    for tool_id, compose_template in result:
+        try:
+            data = yaml.safe_load(compose_template)
+        except Exception:
+            continue
+
+        if not data or "services" not in data:
+            continue
+
+        modified = False
+        for svc in data["services"].values():
+            image = svc.get("image", "")
+            if not image or "linuxserver" not in image:
+                continue
+            if "command" in svc:
+                cmd = svc["command"]
+                if "--bind-addr" in cmd or "--host" in cmd:
+                    del svc["command"]
+                    modified = True
+
+        if modified:
+            updated = yaml.dump(data, default_flow_style=False)
+            conn.execute(
+                sa.text("""
+                    UPDATE tool_types
+                    SET compose_template = :compose_template
+                    WHERE id = :id
+                """),
+                {"compose_template": updated, "id": tool_id},
+            )
+            print(f"Removed broken command override from LSIO template ({tool_id})")
+
+    # Fix existing instance compose files on disk
+    # Use information_schema to check if compose_path column exists
+    col_result = conn.execute(
+        sa.text("""
+            SELECT column_name
+            FROM information_schema.columns
+            WHERE table_name = 'tool_instances'
+            AND column_name = 'compose_path'
+        """)
+    ).fetchone()
+
+    if col_result:
+        result = conn.execute(
+            sa.text("""
+                SELECT id, compose_path
+                FROM tool_instances
+                WHERE compose_path IS NOT NULL
+            """)
+        ).fetchall()
+
+        for instance_id, compose_path in result:
+            path = Path(compose_path)
+            if not path.exists():
+                continue
+            try:
+                content = path.read_text()
+                data = yaml.safe_load(content)
+            except Exception:
+                continue
+
+            if not data or "services" not in data:
+                continue
+
+            modified = False
+            for svc in data["services"].values():
+                image = svc.get("image", "")
+                if not image or "linuxserver" not in image:
+                    continue
+                if "command" in svc:
+                    cmd = svc["command"]
+                    if "--bind-addr" in cmd or "--host" in cmd:
+                        del svc["command"]
+                        modified = True
+
+            if modified:
+                path.write_text(yaml.dump(data, default_flow_style=False))
+                print(
+                    f"Removed broken command override from instance compose "
+                    f"({instance_id})"
+                )
+
+
+def downgrade() -> None:
+    pass

apps/api/alembic/versions/2026_05_29_remove_ssh_keys_mount_from_manifest.py

@@ -0,0 +1,105 @@
+"""remove ssh_keys mount from pi-agent manifest
+
+Revision ID: 2026_05_29_remove_ssh_keys_mount_from_manifest
+Revises: 2026_05_29_add_ssh_key_ids_to_tool_instances
+Create Date: 2026-05-29 14:00:00.000000
+
+"""
+
+import json
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_remove_ssh_keys_mount_from_manifest"
+down_revision: Union[str, None] = "2026_05_29_add_ssh_key_ids_to_tool_instances"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Remove the ssh_keys mount from the pi-agent manifest."""
+    conn = op.get_bind()
+
+    # Get the pi-agent manifest
+    result = conn.execute(
+        sa.text(
+            "SELECT id, manifest FROM tool_definition_manifests WHERE name = 'pi-agent'"
+        )
+    )
+    row = result.fetchone()
+    if not row:
+        return
+
+    manifest_id, manifest_json = row
+    manifest = (
+        manifest_json if isinstance(manifest_json, dict) else json.loads(manifest_json)
+    )
+
+    mounts = manifest.get("mounts", [])
+    original_count = len(mounts)
+
+    # Remove any mount named "ssh_keys"
+    filtered_mounts = [m for m in mounts if m.get("name") != "ssh_keys"]
+
+    if len(filtered_mounts) < original_count:
+        manifest["mounts"] = filtered_mounts
+        conn.execute(
+            sa.text(
+                "UPDATE tool_definition_manifests SET manifest = :manifest WHERE id = :id"
+            ),
+            {
+                "manifest": json.dumps(manifest),
+                "id": manifest_id,
+            },
+        )
+
+
+def downgrade() -> None:
+    """Restore the ssh_keys mount to the pi-agent manifest."""
+    conn = op.get_bind()
+
+    result = conn.execute(
+        sa.text(
+            "SELECT id, manifest FROM tool_definition_manifests WHERE name = 'pi-agent'"
+        )
+    )
+    row = result.fetchone()
+    if not row:
+        return
+
+    manifest_id, manifest_json = row
+    manifest = (
+        manifest_json if isinstance(manifest_json, dict) else json.loads(manifest_json)
+    )
+
+    mounts = manifest.get("mounts", [])
+
+    # Check if ssh_keys mount already exists
+    if any(m.get("name") == "ssh_keys" for m in mounts):
+        return
+
+    # Add the ssh_keys mount back
+    mounts.append(
+        {
+            "name": "ssh_keys",
+            "target": "/home/user/.ssh",
+            "source_type": "ssh_key",
+            "mode": "0700",
+            "file_mode": "0600",
+            "readonly": True,
+        }
+    )
+    manifest["mounts"] = mounts
+
+    conn.execute(
+        sa.text(
+            "UPDATE tool_definition_manifests SET manifest = :manifest WHERE id = :id"
+        ),
+        {
+            "manifest": json.dumps(manifest),
+            "id": manifest_id,
+        },
+    )

apps/api/alembic/versions/2026_06_01_add_workspaces.py

@@ -0,0 +1,81 @@
+"""add workspaces table
+
+Revision ID: 2026_06_01_add_workspaces
+Revises: 2026_05_29_fix_code_server_bind_addr_port
+Create Date: 2026-06-01 10:00:00.000000
+
+"""
+
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_06_01_add_workspaces"
+down_revision: str | None = "2026_05_29_fix_code_server_bind_addr_port"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    # Create workspaces table
+    op.create_table(
+        "workspaces",
+        sa.Column("id", sa.Uuid(as_uuid=True), primary_key=True),
+        sa.Column("name", sa.String(255), nullable=False),
+        sa.Column(
+            "repo_id",
+            sa.Uuid(as_uuid=True),
+            sa.ForeignKey("git_repositories.id", ondelete="CASCADE"),
+            nullable=False,
+        ),
+        sa.Column(
+            "user_id",
+            sa.Uuid(as_uuid=True),
+            sa.ForeignKey("users.id", ondelete="CASCADE"),
+            nullable=False,
+        ),
+        sa.Column("branch", sa.String(255), nullable=False, server_default="main"),
+        sa.Column("path", sa.String(2048), nullable=False),
+        sa.Column("status", sa.String(16), nullable=False, server_default="ready"),
+        sa.Column("last_sync_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "created_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.Column(
+            "updated_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.UniqueConstraint("repo_id", "name", name="uq_workspace_repo_name"),
+        if_not_exists=True,
+    )
+
+    op.create_index("idx_workspaces_repo_id", "workspaces", ["repo_id"])
+    op.create_index("idx_workspaces_user_id", "workspaces", ["user_id"])
+    op.create_index("idx_workspaces_status", "workspaces", ["status"])
+
+    # Add workspace_id to tool_instances
+    op.add_column(
+        "tool_instances",
+        sa.Column(
+            "workspace_id",
+            sa.Uuid(as_uuid=True),
+            sa.ForeignKey("workspaces.id", ondelete="SET NULL"),
+            nullable=True,
+        ),
+    )
+    op.create_index(
+        "idx_tool_instances_workspace_id", "tool_instances", ["workspace_id"]
+    )
+
+
+def downgrade() -> None:
+    op.drop_index("idx_tool_instances_workspace_id", table_name="tool_instances")
+    op.drop_column("tool_instances", "workspace_id")
+    op.drop_table("workspaces")

apps/api/alembic/versions/2026_06_13_make_clone_mode_nullable.py

@@ -0,0 +1,35 @@
+"""make clone_mode nullable
+
+Revision ID: 2026_06_13_make_clone_mode_nullable
+Revises: 86cec91fdb00
+Create Date: 2026-06-13 10:00:00.000000
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision = "2026_06_13_make_clone_mode_nullable"
+down_revision = "86cec91fdb00"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # The workspace-first cleanup no longer writes clone_mode; existing rows
+    # keep their value, but new rows may be NULL.
+    op.alter_column(
+        "tool_instances",
+        "clone_mode",
+        existing_type=sa.String(20),
+        nullable=True,
+    )
+
+
+def downgrade() -> None:
+    op.alter_column(
+        "tool_instances",
+        "clone_mode",
+        existing_type=sa.String(20),
+        nullable=False,
+    )

apps/api/alembic/versions/2026_06_14_104415_add_tool_type_home_directory.py

@@ -0,0 +1,89 @@
+"""add_tool_type_home_directory
+
+Revision ID: 2026_06_14_104415
+Revises: f3d2dc90ba3a
+Create Date: 2026-06-14 10:44:15.000000
+
+"""
+
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_06_14_104415"
+down_revision: Union[str, Sequence[str], None] = "f3d2dc90ba3a"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+tool_types = table(
+    "tool_types",
+    column("id", sa.UUID),
+    column("home_directory", sa.String),
+    column("compose_template", sa.Text),
+    column("dockerfile_template", sa.Text),
+)
+
+OLD_WORKSPACE = "/workspace"
+NEW_WORKSPACE = "/home/user/{{WORKSPACE_NAME}}"
+
+
+def upgrade() -> None:
+    # Add the new column with a default that applies to existing rows.
+    op.add_column(
+        "tool_types",
+        sa.Column(
+            "home_directory",
+            sa.String(255),
+            nullable=False,
+            server_default="/home/user",
+        ),
+    )
+
+    # Rewrite legacy templates that mount the workspace at /workspace so they
+    # use the new configurable home directory and preserve the workspace name.
+    op.execute(
+        sa.update(tool_types)
+        .where(tool_types.c.compose_template.is_not(None))
+        .values(
+            compose_template=sa.func.replace(
+                tool_types.c.compose_template, OLD_WORKSPACE, NEW_WORKSPACE
+            )
+        )
+    )
+    op.execute(
+        sa.update(tool_types)
+        .where(tool_types.c.dockerfile_template.is_not(None))
+        .values(
+            dockerfile_template=sa.func.replace(
+                tool_types.c.dockerfile_template, OLD_WORKSPACE, NEW_WORKSPACE
+            )
+        )
+    )
+
+
+def downgrade() -> None:
+    # Restore the original /workspace strings before dropping the column.
+    op.execute(
+        sa.update(tool_types)
+        .where(tool_types.c.compose_template.is_not(None))
+        .values(
+            compose_template=sa.func.replace(
+                tool_types.c.compose_template, NEW_WORKSPACE, OLD_WORKSPACE
+            )
+        )
+    )
+    op.execute(
+        sa.update(tool_types)
+        .where(tool_types.c.dockerfile_template.is_not(None))
+        .values(
+            dockerfile_template=sa.func.replace(
+                tool_types.c.dockerfile_template, NEW_WORKSPACE, OLD_WORKSPACE
+            )
+        )
+    )
+
+    op.drop_column("tool_types", "home_directory")

apps/api/alembic/versions/2026_06_14_182955_fix_pi_agent_home_directory_mount.py

@@ -0,0 +1,90 @@
+"""fix_pi_agent_home_directory_mount
+
+Revision ID: 2026_06_14_182955
+Revises: fc8f1a20cbf6
+Create Date: 2026-06-14 18:29:55.000000
+
+"""
+
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_06_14_182955"
+down_revision: Union[str, Sequence[str], None] = "fc8f1a20cbf6"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+tool_definition_manifests = table(
+    "tool_definition_manifests",
+    column("id", sa.UUID),
+    column("name", sa.String),
+    column("manifest", sa.JSON),
+)
+
+
+def _find_pi_agent_manifest(conn: sa.Connection) -> tuple[Union[str, None], Union[dict, None]]:
+    result = conn.execute(
+        sa.select(tool_definition_manifests.c.id, tool_definition_manifests.c.manifest)
+        .where(tool_definition_manifests.c.name == "pi-agent")
+    ).fetchone()
+    if result is None:
+        return None, None
+    return result.id, dict(result.manifest)
+
+
+def _update_manifest(conn: sa.Connection, manifest_id: str, manifest: dict) -> None:
+    conn.execute(
+        sa.update(tool_definition_manifests)
+        .where(tool_definition_manifests.c.id == manifest_id)
+        .values(manifest=manifest)
+    )
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+    manifest_id, manifest = _find_pi_agent_manifest(conn)
+    if not manifest_id or not manifest:
+        return
+
+    # Mount the repo under the configured home directory, preserving the repo
+    # directory name via the WORKSPACE_NAME runtime variable.
+    for mount in manifest.get("mounts", []):
+        if mount.get("source_type") == "repo":
+            mount["target"] = "~/{{WORKSPACE_NAME}}"
+
+    # Keep /workspace as a compatibility symlink to the real mount path.
+    runtime = manifest.setdefault("runtime", {})
+    runtime["working_dir"] = "/workspace"
+
+    # Update the startup script to chown the real mount path.
+    scripts = manifest.setdefault("scripts", {})
+    scripts["startup"] = [
+        'if [ -n "$WORKSPACE_NAME" ]; then sudo chown -R user:user "$HOME/$WORKSPACE_NAME" 2>/dev/null || true; fi',
+    ]
+
+    _update_manifest(conn, manifest_id, manifest)
+
+
+def downgrade() -> None:
+    conn = op.get_bind()
+    manifest_id, manifest = _find_pi_agent_manifest(conn)
+    if not manifest_id or not manifest:
+        return
+
+    for mount in manifest.get("mounts", []):
+        if mount.get("source_type") == "repo":
+            mount["target"] = "/workspace"
+
+    runtime = manifest.setdefault("runtime", {})
+    runtime["working_dir"] = "/workspace"
+
+    scripts = manifest.setdefault("scripts", {})
+    scripts["startup"] = [
+        "if [ -d /workspace ]; then sudo chown -R user:user /workspace 2>/dev/null || true; fi",
+    ]
+
+    _update_manifest(conn, manifest_id, manifest)

apps/api/alembic/versions/2026_06_15_090500_remove_pi_agent_explicit_repo_mount.py

@@ -0,0 +1,86 @@
+"""remove pi agent explicit repo mount
+
+Revision ID: 2026_06_15_090500
+Revises: 2026_06_14_182955
+Create Date: 2026-06-15 09:05:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_06_15_090500"
+down_revision: Union[str, Sequence[str], None] = "2026_06_14_182955"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+tool_definition_manifests = table(
+    "tool_definition_manifests",
+    column("id", sa.UUID),
+    column("name", sa.String),
+    column("manifest", sa.JSON),
+)
+
+
+def _find_pi_agent_manifest(
+    conn: sa.Connection,
+) -> tuple[Union[str, None], Union[dict, None]]:
+    result = conn.execute(
+        sa.select(
+            tool_definition_manifests.c.id, tool_definition_manifests.c.manifest
+        ).where(tool_definition_manifests.c.name == "pi-agent")
+    ).fetchone()
+    if result is None:
+        return None, None
+    return result.id, dict(result.manifest)
+
+
+def _update_manifest(conn: sa.Connection, manifest_id: str, manifest: dict) -> None:
+    conn.execute(
+        sa.update(tool_definition_manifests)
+        .where(tool_definition_manifests.c.id == manifest_id)
+        .values(manifest=manifest)
+    )
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+    manifest_id, manifest = _find_pi_agent_manifest(conn)
+    if not manifest_id or not manifest:
+        return
+
+    # The repo mount is now synthesized by compile_compose based on the
+    # instance's repository, so the manifest no longer needs an explicit
+    # repo mount with a {{WORKSPACE_NAME}} placeholder.
+    manifest["mounts"] = [
+        mount
+        for mount in manifest.get("mounts", [])
+        if mount.get("source_type") != "repo"
+    ]
+
+    _update_manifest(conn, manifest_id, manifest)
+
+
+def downgrade() -> None:
+    conn = op.get_bind()
+    manifest_id, manifest = _find_pi_agent_manifest(conn)
+    if not manifest_id or not manifest:
+        return
+
+    mounts = manifest.setdefault("mounts", [])
+    if not any(mount.get("source_type") == "repo" for mount in mounts):
+        mounts.append(
+            {
+                "name": "workspace",
+                "target": "~/{{WORKSPACE_NAME}}",
+                "source_type": "repo",
+                "writable": True,
+                "owner": "user",
+            }
+        )
+
+    _update_manifest(conn, manifest_id, manifest)

apps/api/alembic/versions/2026_06_19_113000_remove_pi_agent_workspace_symlink.py

@@ -0,0 +1,87 @@
+"""remove pi agent workspace symlink
+
+Revision ID: 2026_06_19_113000
+Revises: 2026_06_15_090500
+Create Date: 2026-06-19 11:30:00.000000
+
+"""
+
+from collections.abc import Sequence
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_06_19_113000"
+down_revision: str | Sequence[str] | None = "2026_06_15_090500"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+tool_definition_manifests = table(
+    "tool_definition_manifests",
+    column("id", sa.UUID),
+    column("name", sa.String),
+    column("manifest", sa.JSON),
+)
+
+
+def _find_pi_agent_manifest(
+    conn: sa.Connection,
+) -> tuple[str | None, dict | None]:
+    result = conn.execute(
+        sa.select(
+            tool_definition_manifests.c.id, tool_definition_manifests.c.manifest
+        ).where(tool_definition_manifests.c.name == "pi-agent")
+    ).fetchone()
+    if result is None:
+        return None, None
+    return result.id, dict(result.manifest)
+
+
+def _update_manifest(conn: sa.Connection, manifest_id: str, manifest: dict) -> None:
+    conn.execute(
+        sa.update(tool_definition_manifests)
+        .where(tool_definition_manifests.c.id == manifest_id)
+        .values(manifest=manifest)
+    )
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+    manifest_id, manifest = _find_pi_agent_manifest(conn)
+    if not manifest_id or not manifest:
+        return
+
+    runtime = manifest.setdefault("runtime", {})
+    # The /workspace compatibility symlink is no longer created by the
+    # compiler/entrypoint. Leaving working_dir set to /workspace causes the
+    # container to start in an empty directory. Let compile_compose default
+    # to /home/user/{workspace_name} instead.
+    if runtime.get("working_dir") == "/workspace":
+        del runtime["working_dir"]
+
+    scripts = manifest.setdefault("scripts", {})
+    # Update the startup script to operate on the real repo-named directory.
+    scripts["startup"] = [
+        'if [ -n "$WORKSPACE_NAME" ]; then sudo chown -R user:user "$HOME/$WORKSPACE_NAME" 2>/dev/null || true; fi',
+    ]
+
+    _update_manifest(conn, manifest_id, manifest)
+
+
+def downgrade() -> None:
+    conn = op.get_bind()
+    manifest_id, manifest = _find_pi_agent_manifest(conn)
+    if not manifest_id or not manifest:
+        return
+
+    runtime = manifest.setdefault("runtime", {})
+    runtime["working_dir"] = "/workspace"
+
+    scripts = manifest.setdefault("scripts", {})
+    scripts["startup"] = [
+        "if [ -d /workspace ]; then sudo chown -R user:user /workspace 2>/dev/null || true; fi",
+    ]
+
+    _update_manifest(conn, manifest_id, manifest)

apps/api/alembic/versions/86cec91fdb00_merge_profile_resolver_and_workspaces_.py

@@ -0,0 +1,20 @@
+"""merge profile resolver and workspaces heads
+
+Revision ID: 86cec91fdb00
+Revises: 0014_add_profile_resolver_fields, 2026_06_01_add_workspaces
+Create Date: 2026-06-03 12:48:36.145702
+"""
+
+# revision identifiers, used by Alembic.
+revision = "86cec91fdb00"
+down_revision = ("0014_add_profile_resolver_fields", "2026_06_01_add_workspaces")
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    pass
+
+
+def downgrade() -> None:
+    pass

apps/api/alembic/versions/8c6d1dbd4798_remove_pi_config_and_state_mounts_from_.py

@@ -0,0 +1,112 @@
+"""remove pi config and state mounts from pi-agent manifest
+
+Revision ID: 8c6d1dbd4798
+Revises: 2026_06_13_make_clone_mode_nullable
+Create Date: 2026-06-13 11:21:25.983178
+"""
+
+import json
+
+from alembic import op
+import sqlalchemy as sa
+
+
+
+# revision identifiers, used by Alembic.
+revision = '8c6d1dbd4798'
+down_revision = '2026_06_13_make_clone_mode_nullable'
+branch_labels = None
+depends_on = None
+
+
+def _load_manifest(manifest_json):
+    return manifest_json if isinstance(manifest_json, dict) else json.loads(manifest_json)
+
+
+def upgrade() -> None:
+    """Remove pi_state and pi_config mounts from the pi-agent manifest."""
+    conn = op.get_bind()
+
+    result = conn.execute(
+        sa.text(
+            "SELECT id, manifest FROM tool_definition_manifests WHERE name = 'pi-agent'"
+        )
+    )
+    row = result.fetchone()
+    if not row:
+        return
+
+    manifest_id, manifest_json = row
+    manifest = _load_manifest(manifest_json)
+
+    mounts = manifest.get("mounts", [])
+    original_count = len(mounts)
+
+    filtered_mounts = [
+        m for m in mounts if m.get("name") not in ("pi_state", "pi_config")
+    ]
+
+    if len(filtered_mounts) < original_count:
+        manifest["mounts"] = filtered_mounts
+        conn.execute(
+            sa.text(
+                "UPDATE tool_definition_manifests SET manifest = :manifest WHERE id = :id"
+            ),
+            {
+                "manifest": json.dumps(manifest),
+                "id": manifest_id,
+            },
+        )
+
+
+def downgrade() -> None:
+    """Restore pi_state and pi_config mounts to the pi-agent manifest."""
+    conn = op.get_bind()
+
+    result = conn.execute(
+        sa.text(
+            "SELECT id, manifest FROM tool_definition_manifests WHERE name = 'pi-agent'"
+        )
+    )
+    row = result.fetchone()
+    if not row:
+        return
+
+    manifest_id, manifest_json = row
+    manifest = _load_manifest(manifest_json)
+
+    mounts = manifest.get("mounts", [])
+    existing_names = {m.get("name") for m in mounts}
+
+    if "pi_state" not in existing_names:
+        mounts.append(
+            {
+                "name": "pi_state",
+                "target": "/tmp/.pi/agents",
+                "source_type": "instance",
+                "writable": True,
+            }
+        )
+
+    if "pi_config" not in existing_names:
+        mounts.append(
+            {
+                "name": "pi_config",
+                "target": "/home/user/.pi",
+                "source_type": "git_mount",
+                "git_mount_ref": "dotfiles",
+                "writable": True,
+                "owner": "user",
+            }
+        )
+
+    manifest["mounts"] = mounts
+    conn.execute(
+        sa.text(
+            "UPDATE tool_definition_manifests SET manifest = :manifest WHERE id = :id"
+        ),
+        {
+            "manifest": json.dumps(manifest),
+            "id": manifest_id,
+        },
+    )

apps/api/alembic/versions/fc8f1a20cbf6_merge_home_directory_and_pi_agent_mount_.py

@@ -0,0 +1,23 @@
+"""merge home directory and pi agent mount cleanup heads
+
+Revision ID: fc8f1a20cbf6
+Revises: 2026_06_14_104415, 8c6d1dbd4798
+Create Date: 2026-06-14 11:08:41.273502
+"""
+
+
+
+
+# revision identifiers, used by Alembic.
+revision = 'fc8f1a20cbf6'
+down_revision = ('2026_06_14_104415', '8c6d1dbd4798')
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    pass
+
+
+def downgrade() -> None:
+    pass

apps/api/src/.pi-map.index.md

@@ -0,0 +1,57 @@
+# apps/api/src (index)
+dir: apps/api/src
+
+## role
+Core FastAPI application package that initializes and configures the Headquarter API with database, authentication, logging, and middleware infrastructure.
+## parent
+index: apps/api/.pi-map.index.md
+map: apps/api/.pi-map.md
+## children
+- apps/api/src/.ruff_cache
+  index: apps/api/src/.ruff_cache/.pi-map.index.md
+  map: apps/api/src/.ruff_cache/.pi-map.md
+- apps/api/src/api
+  index: apps/api/src/api/.pi-map.index.md
+  map: apps/api/src/api/.pi-map.md
+- apps/api/src/auth
+  index: apps/api/src/auth/.pi-map.index.md
+  map: apps/api/src/auth/.pi-map.md
+- apps/api/src/headquarter_api.egg-info
+  index: apps/api/src/headquarter_api.egg-info/.pi-map.index.md
+  map: apps/api/src/headquarter_api.egg-info/.pi-map.md
+- apps/api/src/models
+  index: apps/api/src/models/.pi-map.index.md
+  map: apps/api/src/models/.pi-map.md
+- apps/api/src/schemas
+  index: apps/api/src/schemas/.pi-map.index.md
+  map: apps/api/src/schemas/.pi-map.md
+- apps/api/src/scripts
+  index: apps/api/src/scripts/.pi-map.index.md
+  map: apps/api/src/scripts/.pi-map.md
+- apps/api/src/seeds
+  index: apps/api/src/seeds/.pi-map.index.md
+  map: apps/api/src/seeds/.pi-map.md
+- apps/api/src/services
+  index: apps/api/src/services/.pi-map.index.md
+  map: apps/api/src/services/.pi-map.md
+- apps/api/src/utils
+  index: apps/api/src/utils/.pi-map.index.md
+  map: apps/api/src/utils/.pi-map.md
+## files
+- __init__.py
+- config.py
+- database.py
+- logging_config.py
+- main.py
+## links
+index: apps/api/src/.pi-map.index.md
+map: apps/api/src/.pi-map.md
+## workflows
+- change src behavior
+  read: __init__.py, config.py, database.py
+- change src config
+  read: config.py, logging_config.py
+- explore src subdirectories
+  index: apps/api/src/.ruff_cache/.pi-map.index.md, apps/api/src/api/.pi-map.index.md, apps/api/src/auth/.pi-map.index.md
+## dirty
+-

apps/api/src/.pi-map.md

@@ -0,0 +1,35 @@
+# apps/api/src
+dir: apps/api/src
+
+index: apps/api/src/.pi-map.index.md
+
+## role
+Core FastAPI application package that initializes and configures the Headquarter API with database, authentication, logging, and middleware infrastructure.
+## files
+- __init__.py | Marks the directory as a Python package for the Headquarter API.
+- config.py | Defines application configuration settings using pydantic-settings, including database connectivity, Authentik SSO, JWT, session, and domain-based URL resolution. | exp: class:Settings, func:build_database_url(user: str, password: str, host: str, port: int, database: str) → str | dep: pydantic, pydantic_settings
+- database.py | Configures an async SQLAlchemy database engine/session and provides a retry-based initialization function that runs Alembic migrations via subprocess. | exp: func:init_database(max_retries, retry_delay) → bool, call:range, call:engine.connect, call:test_conn.execute, call:text, call:test_conn.close, call:logger.info, call:asyncio.get_event_loop().run_in_executor, call:subprocess.run, call:os.path.dirname, call:os.path.abspath, call:logger.debug, call:logger.error, call:asyncio.sleep, call:str(exc).lower, call:logger.warning | dep: asyncio, logging, os, subprocess, sqlalchemy.ext.asyncio, sqlalchemy.pool, src.config, sqlalchemy
+- logging_config.py | Configures structured JSON logging with correlation ID injection and provides ASGI middleware for logging HTTP requests, responses, and unhandled exceptions. | exp: class:CorrelationIdFilter, method:filter(self, record: logging.LogRecord) → bool, call:get_correlation_id, class:JSONFormatter, method:format(self, record: logging.LogRecord) → str, call:self.formatTime, call:record.getMessage, call:getattr, call:self.formatException, call:json.dumps, method:formatTime(self, record: logging.LogRecord, datefmt) → str, call:time.strftime, call:time.gmtime, class:RequestLoggingMiddleware, method:dispatch(self, request: Request, call_next: Callable) → Response, call:time.time, call:logger.info, call:call_next, call:int, call:logger.error, call:type, call:traceback.format_exc, class:ExceptionLoggingMiddleware, method:dispatch(self, request: Request, call_next: Callable) → Response, call:call_next, call:logger.critical, call:traceback.format_exc, func:configure_logging(level) → None, call:JSONFormatter, call:logging.StreamHandler, call:console_handler.setFormatter, call:console_handler.addFilter, call:CorrelationIdFilter, call:root_logger.setLevel, call:logging.getLogger("uvicorn").setLevel, call:logging.getLogger("uvicorn.access").setLevel, call:logging.getLogger("sqlalchemy.engine").setLevel, call:logger.info, call:logging.getLevelName | dep: json, logging, sys, time, traceback, collections.abc, fastapi, starlette.middleware.base, src.services.shared.correlation, starlette
+- main.py | Initializes and configures the FastAPI application, setting up middleware, routers, database connections, and lifecycle event handlers for the Headquarter API. | exp: func:_sanitize_validation_errors(errors), call:error.get, call:str, call:ctx.items, call:isinstance, call:type, call:sanitized.append, func:validation_exception_handler(request: Request, exc: RequestValidationError), call:exc.errors, call:logger.warning, call:_sanitize_validation_errors, call:JSONResponse, func:on_startup(), call:logger.info, call:init_database, call:logger.error, call:sys.exit, call:_health_monitor.start, call:seed_builtin_tool_types, func:on_shutdown(), call:logger.info, call:_health_monitor.stop | dep: logging, os, fastapi, fastapi.exceptions, fastapi.middleware.cors, fastapi.responses, fastapi.staticfiles, src.api.config, src.api.project, src.api.system, src.api.tool, src.api.user, src.api.workspace, src.config, src.models, src.database, src.logging_config, src.seeds.builtin_tool_types, src.services.instance, src.services.shared, sys, src.api, src.seeds, src.services
+## arch
+Layered architecture using Pydantic-settings for configuration, async SQLAlchemy with Alembic migrations, structured JSON logging with correlation ID tracking, and FastAPI lifecycle management with dependency injection for cross-cutting concerns.
+## tags
+src, logging, database, call:logger.info, api, middleware, filter, call:logging.get
+## symbols
+- Settings
+- CorrelationIdFilter
+- JSONFormatter
+- RequestLoggingMiddleware
+- ExceptionLoggingMiddleware
+- build_database_url
+- init_database
+- filter
+## workflows
+- change src behavior
+  read: __init__.py, config.py, database.py
+- change src config
+  read: config.py, logging_config.py
+- explore src subdirectories
+  index: apps/api/src/.ruff_cache/.pi-map.index.md, apps/api/src/api/.pi-map.index.md, apps/api/src/auth/.pi-map.index.md
+## dirty
+-

apps/api/src/api/.pi-map.index.md

@@ -0,0 +1,43 @@
+# apps/api/src/api (index)
+dir: apps/api/src/api
+
+## role
+Defines the core API router package with reusable Pydantic validation utilities for container and filesystem-related API schemas.
+## parent
+index: apps/api/src/.pi-map.index.md
+map: apps/api/src/.pi-map.md
+## children
+- apps/api/src/api/.ruff_cache
+  index: apps/api/src/api/.ruff_cache/.pi-map.index.md
+  map: apps/api/src/api/.ruff_cache/.pi-map.md
+- apps/api/src/api/config
+  index: apps/api/src/api/config/.pi-map.index.md
+  map: apps/api/src/api/config/.pi-map.md
+- apps/api/src/api/project
+  index: apps/api/src/api/project/.pi-map.index.md
+  map: apps/api/src/api/project/.pi-map.md
+- apps/api/src/api/system
+  index: apps/api/src/api/system/.pi-map.index.md
+  map: apps/api/src/api/system/.pi-map.md
+- apps/api/src/api/tool
+  index: apps/api/src/api/tool/.pi-map.index.md
+  map: apps/api/src/api/tool/.pi-map.md
+- apps/api/src/api/user
+  index: apps/api/src/api/user/.pi-map.index.md
+  map: apps/api/src/api/user/.pi-map.md
+- apps/api/src/api/workspace
+  index: apps/api/src/api/workspace/.pi-map.index.md
+  map: apps/api/src/api/workspace/.pi-map.md
+## files
+- __init__.py
+- shared_validators.py
+## links
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## workflows
+- change api behavior
+  read: __init__.py, shared_validators.py
+- explore api subdirectories
+  index: apps/api/src/api/.ruff_cache/.pi-map.index.md, apps/api/src/api/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md
+## dirty
+-

apps/api/src/api/.pi-map.md

@@ -0,0 +1,30 @@
+# apps/api/src/api
+dir: apps/api/src/api
+
+index: apps/api/src/api/.pi-map.index.md
+
+## role
+Defines the core API router package with reusable Pydantic validation utilities for container and filesystem-related API schemas.
+## files
+- __init__.py | Marks the directory as a Python package for API routers.
+- shared_validators.py | Provides reusable Pydantic validator functions for validating mount paths, file contents, environment variables, and volume mounts in API schemas. | exp: func:validate_mount_path(v: str | None) → str | None, call:v.startswith, raise:ValueError, func:validate_files(v: dict | None, max_size_bytes) → dict | None, call:v.items, call:path.startswith, call:len, call:content.encode, raise:ValueError, func:validate_env_vars(v: dict | None) → dict | None, call:isinstance, raise:ValueError, func:validate_volumes(v: list | None) → list | None, call:isinstance, call:enumerate, raise:ValueError
+## arch
+Modular package structure separating router organization from shared cross-cutting validation concerns using Pydantic validators.
+## tags
+validate, raise:value, error, call:isinstance, mount, api, init, path
+## symbols
+- validate_mount_path
+- validate_files
+- validate_env_vars
+- validate_volumes
+- call:v.startswith
+- raise:ValueError
+- call:v.items
+- call:path.startswith
+## workflows
+- change api behavior
+  read: __init__.py, shared_validators.py
+- explore api subdirectories
+  index: apps/api/src/api/.ruff_cache/.pi-map.index.md, apps/api/src/api/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md
+## dirty
+-

apps/api/src/api/__init__.py

@@ -1,4 +1 @@
-from src.api.auth import router as auth_router
-from src.api.users import router as users_router
-
-__all__ = ["auth_router", "users_router"]
+"""API routers package."""

apps/api/src/api/config/.pi-map.index.md

@@ -0,0 +1,24 @@
+# apps/api/src/api/config (index)
+dir: apps/api/src/api/config
+
+## role
+Provides FastAPI API endpoints for managing user configuration settings and config profiles.
+## parent
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- config_profiles.py
+- user_config.py
+## links
+index: apps/api/src/api/config/.pi-map.index.md
+map: apps/api/src/api/config/.pi-map.md
+## workflows
+- change config behavior
+  read: __init__.py, config_profiles.py, user_config.py
+- change config config
+  read: config_profiles.py, user_config.py
+## dirty
+-

apps/api/src/api/config/.pi-map.md

@@ -0,0 +1,31 @@
+# apps/api/src/api/config
+dir: apps/api/src/api/config
+
+index: apps/api/src/api/config/.pi-map.index.md
+
+## role
+Provides FastAPI API endpoints for managing user configuration settings and config profiles.
+## files
+- __init__.py | Aggregates and exports config-related API routers for module-level access | dep: src.api.config.config_profiles, src.api.config.user_config
+- config_profiles.py | FastAPI router providing CRUD endpoints for user-owned config profiles with include resolution, default profile management, and git URL validation. | exp: func:list_config_profiles(project_id, tool_type_id, current_user_id, session), call:select(ConfigProfile) .where(ConfigProfile.user_id == user_uuid) .options, call:selectinload, call:uuid.UUID, call:conditions.append, call:ConfigProfile.project_id.is_, call:ConfigProfile.tool_type_id.is_, call:query.where, call:or_, call:session.execute, call:result.scalars().all, call:profile_to_response, func:create_config_profile(data: ConfigProfileCreate, current_user_id, session), call:create_profile, call:logger.debug, call:profile_to_response, func:get_config_profile(profile_id: str, current_user_id, session), call:get_profile_with_includes, call:uuid.UUID, call:profile_to_response, raise:HTTPException, func:update_config_profile(profile_id: str, data: ConfigProfileUpdate, current_user_id, session), call:get_profile_with_includes, call:uuid.UUID, call:update_profile, call:logger.debug, call:profile_to_response, raise:HTTPException, func:delete_config_profile(profile_id: str, current_user_id, session), call:get_profile_with_includes, call:uuid.UUID, call:session.delete, call:session.commit, call:logger.debug, raise:HTTPException, func:update_profile_includes_endpoint(profile_id: str, data: ConfigProfileIncludeUpdate, current_user_id, session), call:get_profile_with_includes, call:uuid.UUID, call:update_includes, call:session.execute, call:select(ConfigProfileInclude).where, call:inc_result.scalars().all, call:logger.debug, call:profile_to_response, call:list, raise:HTTPException, func:preview_config_profile(profile_id: str, current_user_id, session), call:get_profile_with_includes, call:uuid.UUID, call:resolve_profile, call:resolved_profile_to_dict, raise:HTTPException, func:resolve_default_profile_endpoint(project_id, tool_type_id, current_user_id, session), call:resolve_default_profile, call:uuid.UUID, func:get_default_profiles_endpoint(user_id, session) → dict, call:session.execute, call:select(UserConfig).where, call:result.scalar_one_or_none, func:set_default_profiles_endpoint(data: DefaultProfilesUpdate, user_id, session) → dict, call:validate_default_profiles, call:get_or_create_user_config, call:session.commit, call:session.refresh, func:get_default_profile_for_tool_type_endpoint(tool_type_id: str, user_id, session) → dict, call:session.execute, call:select(UserConfig).where, call:result.scalar_one_or_none, call:user_config.default_profiles.get, func:validate_git_url_endpoint(data: ValidateGitUrlRequest, current_user_id, session) → ValidateGitUrlResponse, call:validate_git_url | dep: logging, uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, sqlalchemy.orm, src.auth.dependencies, src.models, src.schemas.config, src.services.config.config_profile_resolver, src.services.config.crud_service, src.services.config.resolver_service
+- user_config.py | Provides FastAPI endpoints for retrieving and updating user configuration settings with automatic record creation. | exp: func:_get_or_create_config(session: AsyncSession, user_id: uuid.UUID) → UserConfig, call:session.execute, call:select(UserConfig).where, call:result.scalar_one_or_none, call:UserConfig, call:session.add, call:session.commit, call:session.refresh, func:get_user_config(user_id, session) → UserConfigResponse, call:_get_user, call:_get_or_create_config, call:UserConfigResponse.model_validate, func:update_user_config(data: UserConfigUpdate, user_id, session) → UserConfigResponse, call:_get_user, call:_get_or_create_config, call:data.model_dump, call:logger.debug, call:session.commit, call:session.refresh, call:UserConfigResponse.model_validate | dep: logging, uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.schemas.user
+## arch
+Modular router-based architecture using FastAPI with separate route modules for distinct config domains (profiles vs. user settings), CRUD patterns, and include resolution for hierarchical config.
+## tags
+config, profile, get, user, call:uuid.uuid, includes, or, default
+## symbols
+- list_config_profiles
+- create_config_profile
+- get_config_profile
+- update_config_profile
+- delete_config_profile
+- update_profile_includes_endpoint
+- preview_config_profile
+- resolve_default_profile_endpoint
+## workflows
+- change config behavior
+  read: __init__.py, config_profiles.py, user_config.py
+- change config config
+  read: config_profiles.py, user_config.py
+## dirty
+-

apps/api/src/api/config/__init__.py

@@ -0,0 +1,6 @@
+"""Config API routers module."""
+
+from src.api.config.config_profiles import router as config_profiles_router
+from src.api.config.user_config import router as user_config_router
+
+__all__ = ["config_profiles_router", "user_config_router"]

apps/api/src/api/config/config_profiles.py

@@ -0,0 +1,422 @@
+"""Config profile API endpoints."""
+
+import logging
+import os
+import uuid
+from pathlib import Path
+
+from fastapi import APIRouter, Depends, HTTPException, Query, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.orm import selectinload
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.config import Settings
+from src.models import ConfigProfile, ConfigProfileInclude, ToolInstance, UserConfig
+from src.schemas.config import (
+    ConfigProfileCreate,
+    ConfigProfileIncludeUpdate,
+    ConfigProfileResponse,
+    ConfigProfileUpdate,
+    DefaultProfilesUpdate,
+    ValidateGitUrlRequest,
+    ValidateGitUrlResponse,
+)
+from src.services.config.config_profile_resolver import (
+    ConfigProfileCycleError,
+    apply_resolved_profile,
+    resolve_profile,
+    resolved_profile_to_dict,
+)
+from src.services.config.crud_service import (
+    create_profile,
+    get_or_create_user_config,
+    get_profile_with_includes,
+    profile_to_response,
+    update_includes,
+    update_profile,
+    validate_default_profiles,
+)
+from src.services.config.resolver_service import (
+    resolve_default_profile,
+    validate_git_url,
+)
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
+
+
+def _canonical_profile_response(profile: ConfigProfile) -> dict:
+    """Return profile data with edits from its shared working copy."""
+    response = profile_to_response(profile)
+    root = Path(Settings().instance_base_path) / "config-profiles" / str(profile.id)
+
+    def read_file(path: Path, fallback: str) -> str:
+        try:
+            return path.read_text() if path.is_file() else fallback
+        except OSError:
+            return fallback
+
+    response["files"] = {
+        relative_path: read_file(root / "files" / relative_path, content)
+        for relative_path, content in response["files"].items()
+    }
+    response["mounts"] = [dict(mount) for mount in response["mounts"]]
+    for mount in response["mounts"]:
+        mount_root = root / "mounts" / mount["target"].lstrip("/").replace("/", "_")
+        mount["files"] = {
+            relative_path: read_file(mount_root / relative_path, content)
+            for relative_path, content in mount.get("files", {}).items()
+        }
+    return response
+
+
+async def _running_profile_outcomes(
+    session: AsyncSession, profile_id: uuid.UUID
+) -> list[dict[str, str]]:
+    """Report running instances that must restart to adopt a profile revision."""
+    result = await session.execute(
+        select(ToolInstance).where(ToolInstance.status == "running")
+    )
+    outcomes: list[dict[str, str]] = []
+    for instance in result.scalars().all():
+        if instance.selected_config_profile_id is None:
+            continue
+        resolved = await resolve_profile(session, instance.selected_config_profile_id)
+        dependencies = {resolved.profile_id} | {
+            uuid.UUID(item["id"])
+            for item in resolved.included_profiles
+            if item.get("id")
+        }
+        if profile_id in dependencies:
+            outcomes.append(
+                {
+                    "instance_id": str(instance.id),
+                    "status": "restart_required",
+                    "reason": "Existing instance must restart to adopt shared profile mounts",
+                }
+            )
+    return outcomes
+
+
+@router.get("", response_model=list[ConfigProfileResponse])
+async def list_config_profiles(
+    project_id: str | None = Query(None, description="Filter by project compatibility"),
+    tool_type_id: str | None = Query(
+        None, description="Filter by tool type compatibility"
+    ),
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """List config profiles, optionally filtered by compatibility."""
+    user_uuid = current_user_id
+    query = (
+        select(ConfigProfile)
+        .where(ConfigProfile.user_id == user_uuid)
+        .options(selectinload(ConfigProfile.includes))
+    )
+
+    if project_id or tool_type_id:
+        from sqlalchemy import or_
+
+        project_uuid = uuid.UUID(project_id) if project_id else None
+        tool_uuid = uuid.UUID(tool_type_id) if tool_type_id else None
+
+        conditions: list = []
+        conditions.append(
+            (ConfigProfile.project_id.is_(None))
+            & (ConfigProfile.tool_type_id.is_(None))
+        )
+        if project_uuid:
+            conditions.append(ConfigProfile.project_id == project_uuid)
+        if tool_uuid:
+            conditions.append(ConfigProfile.tool_type_id == tool_uuid)
+        if project_uuid and tool_uuid:
+            conditions.append(
+                (ConfigProfile.project_id == project_uuid)
+                & (ConfigProfile.tool_type_id == tool_uuid)
+            )
+
+        query = query.where(or_(*conditions))
+
+    result = await session.execute(query)
+    profiles = result.scalars().all()
+    return [_canonical_profile_response(profile) for profile in profiles]
+
+
+@router.post(
+    "", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED
+)
+async def create_config_profile(
+    data: ConfigProfileCreate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Create a new config profile."""
+    profile = await create_profile(session, current_user_id, data)
+    logger.debug("Created config profile %s for user %s", profile.id, current_user_id)
+    return profile_to_response(profile)
+
+
+@router.get("/{profile_id}", response_model=ConfigProfileResponse)
+async def get_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Get a config profile by ID."""
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+    return _canonical_profile_response(profile)
+
+
+@router.put("/{profile_id}", response_model=ConfigProfileResponse)
+async def update_config_profile(
+    profile_id: str,
+    data: ConfigProfileUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update a config profile."""
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    profile = await update_profile(session, profile, data)
+    resolved = await resolve_profile(session, profile.id)
+    apply_resolved_profile(
+        os.path.join(Settings().instance_base_path, "profile-refresh"),
+        resolved,
+    )
+    response = _canonical_profile_response(profile)
+    response["refresh_outcomes"] = await _running_profile_outcomes(session, profile.id)
+    logger.debug("Updated config profile %s", profile.id)
+    return response
+
+
+@router.post("/{profile_id}/refresh-git-mounts")
+async def refresh_profile_git_mounts(
+    profile_id: str,
+    confirm_destructive_refresh: bool = False,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Destructively refresh profile Git working copies used by instances."""
+    if not confirm_destructive_refresh:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail="Confirm destructive Git refresh before replacing local edits",
+        )
+
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    # Import lazily: instance_service imports tool schemas that transitively
+    # load API routers, so importing it during router initialization cycles.
+    from src.services.tool.instance_service import resolve_git_mounts
+
+    outcomes = await _running_profile_outcomes(session, profile.id)
+    for outcome in outcomes:
+        instance = await session.get(ToolInstance, uuid.UUID(outcome["instance_id"]))
+        if (
+            instance is None
+            or not instance.compose_path
+            or instance.selected_config_profile_id is None
+        ):
+            continue
+        resolved = await resolve_profile(session, instance.selected_config_profile_id)
+        await resolve_git_mounts(
+            session,
+            resolved,
+            os.path.dirname(instance.compose_path),
+        )
+        outcome["status"] = "refreshed"
+        outcome["reason"] = "Canonical Git mount source refreshed in place"
+    return {"refresh_outcomes": outcomes}
+
+
+@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Delete a config profile."""
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    outcomes = await _running_profile_outcomes(session, profile.id)
+    if outcomes:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail={
+                "message": "Profile is still used by running instances",
+                "outcomes": outcomes,
+            },
+        )
+
+    await session.delete(profile)
+    await session.commit()
+
+    logger.debug("Deleted config profile %s", profile_id)
+    return None
+
+
+@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
+async def update_profile_includes_endpoint(
+    profile_id: str,
+    data: ConfigProfileIncludeUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update the ordered includes for a config profile."""
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    included_uuids = [uuid.UUID(inc_id) for inc_id in data.includes]
+    profile = await update_includes(session, profile, included_uuids, current_user_id)
+
+    inc_result = await session.execute(
+        select(ConfigProfileInclude).where(
+            ConfigProfileInclude.profile_id == profile.id
+        )
+    )
+    direct_includes = inc_result.scalars().all()
+
+    logger.debug("Updated includes for config profile %s", profile.id)
+    return profile_to_response(profile, list(direct_includes))
+
+
+@router.get("/{profile_id}/preview")
+async def preview_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Preview the resolved output of a config profile."""
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    try:
+        resolved = await resolve_profile(session, profile.id)
+    except ConfigProfileCycleError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=str(exc),
+        )
+
+    return resolved_profile_to_dict(resolved)
+
+
+@router.get("/defaults/resolve")
+async def resolve_default_profile_endpoint(
+    project_id: str = Query(..., description="Project ID"),
+    tool_type_id: str = Query(..., description="Tool type ID"),
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Resolve the default config profile for a project/tool combination."""
+    return await resolve_default_profile(
+        session,
+        current_user_id,
+        uuid.UUID(project_id),
+        uuid.UUID(tool_type_id),
+    )
+
+
+@router.get("/defaults")
+async def get_default_profiles_endpoint(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get all default profile mappings for the current user."""
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
+    )
+    user_config = result.scalar_one_or_none()
+    return {"default_profiles": user_config.default_profiles if user_config else {}}
+
+
+@router.put("/defaults")
+async def set_default_profiles_endpoint(
+    data: DefaultProfilesUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Set default profile mappings for the current user."""
+    await validate_default_profiles(session, user_id, data.default_profiles)
+    user_config = await get_or_create_user_config(session, user_id)
+    user_config.config = {
+        **user_config.config,
+        "default_profiles": data.default_profiles,
+    }
+    await session.commit()
+    await session.refresh(user_config)
+    return {"default_profiles": user_config.default_profiles}
+
+
+@router.get("/defaults/{tool_type_id}")
+async def get_default_profile_for_tool_type_endpoint(
+    tool_type_id: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get the default profile ID for a specific tool type."""
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
+    )
+    user_config = result.scalar_one_or_none()
+    profile_id = user_config.default_profiles.get(tool_type_id) if user_config else None
+    return {"tool_type_id": tool_type_id, "profile_id": profile_id}
+
+
+@router.post("/validate-git-url", response_model=ValidateGitUrlResponse)
+async def validate_git_url_endpoint(
+    data: ValidateGitUrlRequest,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> ValidateGitUrlResponse:
+    """Validate a git remote URL and list available branches."""
+    return await validate_git_url(session, current_user_id, data.url, data.ssh_key_id)

apps/api/src/api/config/user_config.py

@@ -2,19 +2,21 @@ import logging
 import uuid
 
 from fastapi import APIRouter, Depends
-from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
-from src.models.user_config import UserConfig
+from src.models import UserConfig
+from src.schemas.user import UserConfigResponse, UserConfigUpdate
 
 logger = logging.getLogger(__name__)
 
 router = APIRouter(prefix="/users/me", tags=["user-config"])
 
 
-async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> UserConfig:
+async def _get_or_create_config(
+    session: AsyncSession, user_id: uuid.UUID
+) -> UserConfig:
     """Get or create user config record.
 
     Args:
@@ -24,7 +26,9 @@ async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> Us
     Returns:
         The user's config, creating a new one if it doesn't exist.
     """
-    result = await session.execute(select(UserConfig).where(UserConfig.user_id == user_id))
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
+    )
     config = result.scalar_one_or_none()
     if config is None:
         config = UserConfig(user_id=user_id, config={})
@@ -34,24 +38,6 @@ async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> Us
     return config
 
 
-class UserConfigResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    default_editor: str | None = None
-    theme: str = "system"
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-
-
-class UserConfigUpdate(BaseModel):
-    default_editor: str | None = None
-    theme: str | None = None
-    git_user_name: str | None = None
-    git_user_email: str | None = None
-    last_session_id: str | None = None
-
-
 @router.get(
     "/config",
     response_model=UserConfigResponse,

apps/api/src/api/config_folders.py

@@ -1,337 +0,0 @@
-"""Config folder API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, status
-from pydantic import BaseModel, Field, field_validator
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.api.shared_validators import validate_files as _validate_files, validate_mount_path as _validate_mount_path
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.config_folder import ConfigFolder
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/config-folders", tags=["config-folders"])
-
-
-class ConfigFolderCreate(BaseModel):
-    name: str = Field(description="Folder name (unique per user)")
-    description: str | None = Field(default=None, description="Optional description")
-    mount_path: str = Field(description="Default mount path in container")
-    files: dict = Field(default_factory=dict, description="Files as {path: content}")
-
-    @field_validator("mount_path")
-    @classmethod
-    def validate_mount_path(cls, v: str) -> str:
-        return _validate_mount_path(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict) -> dict:
-        return _validate_files(v)
-
-
-class ConfigFolderUpdate(BaseModel):
-    name: str | None = Field(default=None, description="Folder name")
-    description: str | None = Field(default=None, description="Optional description")
-    mount_path: str | None = Field(default=None, description="Default mount path")
-    files: dict | None = Field(default=None, description="Files as {path: content}")
-    is_active: bool | None = Field(default=None, description="Active/inactive toggle")
-
-    @field_validator("mount_path")
-    @classmethod
-    def validate_mount_path(cls, v: str | None) -> str | None:
-        return _validate_mount_path(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict | None) -> dict | None:
-        return _validate_files(v)
-
-
-class ProjectOverrideCreate(BaseModel):
-    mount_path: str | None = Field(default=None, description="Override mount path")
-    files: dict = Field(default_factory=dict, description="Override files")
-
-    @field_validator("mount_path")
-    @classmethod
-    def validate_mount_path(cls, v: str | None) -> str | None:
-        return _validate_mount_path(v)
-
-
-class ConfigFolderResponse(BaseModel):
-    id: str
-    user_id: str
-    name: str
-    description: str | None
-    mount_path: str
-    files: dict
-    project_overrides: dict | None
-    is_active: bool
-    created_at: str
-    updated_at: str
-
-
-@router.get("", summary="List config folders", description="Get all config folders for the current user.")
-async def list_config_folders(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """List config folders for the current user."""
-    query = select(ConfigFolder).where(ConfigFolder.user_id == user_id)
-    result = await session.execute(query)
-    folders = result.scalars().all()
-    
-    return {
-        "folders": [
-            {
-                "id": str(f.id),
-                "user_id": str(f.user_id),
-                "name": f.name,
-                "description": f.description,
-                "mount_path": f.mount_path,
-                "files": f.files,
-                "project_overrides": f.project_overrides,
-                "is_active": f.is_active,
-                "created_at": f.created_at.isoformat() if f.created_at else None,
-                "updated_at": f.updated_at.isoformat() if f.updated_at else None,
-            }
-            for f in folders
-        ]
-    }
-
-
-@router.post("", summary="Create config folder", description="Create a new config folder.", status_code=status.HTTP_201_CREATED)
-async def create_config_folder(
-    data: ConfigFolderCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a config folder."""
-    # Check for duplicate name
-    existing = await session.scalar(
-        select(ConfigFolder).where(
-            ConfigFolder.user_id == user_id,
-            ConfigFolder.name == data.name,
-        )
-    )
-    if existing:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"config folder with name '{data.name}' already exists"
-        )
-    
-    folder = ConfigFolder(
-        user_id=user_id,
-        name=data.name,
-        description=data.description,
-        mount_path=data.mount_path,
-        files=data.files,
-    )
-    session.add(folder)
-    await session.commit()
-    await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "user_id": str(folder.user_id),
-        "name": folder.name,
-        "description": folder.description,
-        "mount_path": folder.mount_path,
-        "files": folder.files,
-        "project_overrides": folder.project_overrides,
-        "is_active": folder.is_active,
-        "created_at": folder.created_at.isoformat() if folder.created_at else None,
-        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
-    }
-
-
-@router.put("/{folder_id}", summary="Update config folder", description="Update an existing config folder.")
-async def update_config_folder(
-    folder_id: uuid.UUID,
-    data: ConfigFolderUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Update a config folder."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    if data.name is not None:
-        folder.name = data.name
-    if data.description is not None:
-        folder.description = data.description
-    if data.mount_path is not None:
-        folder.mount_path = data.mount_path
-    if data.files is not None:
-        folder.files = data.files
-    if data.is_active is not None:
-        folder.is_active = data.is_active
-    
-    await session.commit()
-    await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "user_id": str(folder.user_id),
-        "name": folder.name,
-        "description": folder.description,
-        "mount_path": folder.mount_path,
-        "files": folder.files,
-        "project_overrides": folder.project_overrides,
-        "is_active": folder.is_active,
-        "created_at": folder.created_at.isoformat() if folder.created_at else None,
-        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
-    }
-
-
-@router.delete("/{folder_id}", summary="Delete config folder", description="Delete a config folder.", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_config_folder(
-    folder_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Delete a config folder."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    await session.delete(folder)
-    await session.commit()
-
-
-class ProjectOverrideWithId(ProjectOverrideCreate):
-    project_id: uuid.UUID = Field(description="Project ID for the override")
-
-
-@router.get("/{folder_id}", summary="Get config folder by ID", description="Get a single config folder by its ID.")
-async def get_config_folder(
-    folder_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get a config folder by ID."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    return {
-        "id": str(folder.id),
-        "user_id": str(folder.user_id),
-        "name": folder.name,
-        "description": folder.description,
-        "mount_path": folder.mount_path,
-        "files": folder.files,
-        "project_overrides": folder.project_overrides,
-        "is_active": folder.is_active,
-        "created_at": folder.created_at.isoformat() if folder.created_at else None,
-        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
-    }
-
-
-@router.post("/{folder_id}/overrides", summary="Add project override", description="Add a project override to a config folder.")
-async def add_project_override(
-    folder_id: uuid.UUID,
-    data: ProjectOverrideWithId,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Add a project override to a config folder."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    # Initialize project_overrides if None
-    if folder.project_overrides is None:
-        folder.project_overrides = {}
-    
-    # Add/update override
-    override_data = {}
-    if data.mount_path is not None:
-        override_data["mount_path"] = data.mount_path
-    if data.files is not None:
-        override_data["files"] = data.files
-    
-    # Use a copy to trigger SQLAlchemy change detection on JSONB
-    current_overrides = dict(folder.project_overrides or {})
-    current_overrides[str(data.project_id)] = override_data
-    folder.project_overrides = current_overrides
-    
-    await session.commit()
-    await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "project_overrides": folder.project_overrides,
-    }
-
-
-@router.put("/{folder_id}/overrides/{project_id}", summary="Update project override", description="Update a project override.")
-async def update_project_override(
-    folder_id: uuid.UUID,
-    project_id: uuid.UUID,
-    data: ProjectOverrideCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Update a project override."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    # Initialize project_overrides if None
-    if folder.project_overrides is None:
-        folder.project_overrides = {}
-    
-    # Update override
-    current_overrides = dict(folder.project_overrides or {})
-    override_data = current_overrides.get(str(project_id), {})
-    if data.mount_path is not None:
-        override_data["mount_path"] = data.mount_path
-    if data.files is not None:
-        override_data["files"] = data.files
-    
-    current_overrides[str(project_id)] = override_data
-    folder.project_overrides = current_overrides
-    
-    # Mark the field as modified to ensure SQLAlchemy detects the change
-    from sqlalchemy.orm.attributes import flag_modified
-    flag_modified(folder, "project_overrides")
-    
-    await session.commit()
-    await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "project_overrides": folder.project_overrides,
-    }
-
-
-@router.delete("/{folder_id}/overrides/{project_id}", summary="Remove project override", description="Remove a project override.")
-async def remove_project_override(
-    folder_id: uuid.UUID,
-    project_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Remove a project override."""
-    folder = await session.get(ConfigFolder, folder_id)
-    if folder is None or folder.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
-    
-    # Remove override if exists
-    current_overrides = dict(folder.project_overrides or {})
-    if str(project_id) in current_overrides:
-        del current_overrides[str(project_id)]
-        folder.project_overrides = current_overrides
-        await session.commit()
-        await session.refresh(folder)
-    
-    return {
-        "id": str(folder.id),
-        "project_overrides": folder.project_overrides or {},
-    }

apps/api/src/api/config_profiles.py

@@ -1,723 +0,0 @@
-"""Config profile API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, Query, status
-from pydantic import BaseModel, Field, field_validator
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-from sqlalchemy.orm import selectinload
-
-from src.api.shared_validators import validate_env_vars as _validate_env_vars
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
-from src.models.project import Project
-from src.models.tool_type import ToolType
-from src.services.config_profile_resolver import (
-    ConfigProfileCycleError,
-    check_include_cycle,
-    resolve_profile,
-    resolved_profile_to_dict,
-)
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
-
-MAX_PROFILE_SIZE_MB = 10
-MAX_PROFILE_SIZE_BYTES = MAX_PROFILE_SIZE_MB * 1024 * 1024
-
-
-def _validate_uuid(v: str | None) -> str | None:
-    if v is None:
-        return v
-    try:
-        uuid.UUID(v)
-    except ValueError:
-        raise ValueError(f"Invalid UUID: {v}")
-    return v
-
-
-def _calculate_profile_size(data: dict) -> int:
-    """Calculate approximate serialized size of profile data."""
-    total = 0
-    for key, value in data.get("env_vars", {}).items():
-        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
-    for key, value in data.get("runtime_hints", {}).items():
-        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
-    for mount in data.get("mounts", []):
-        total += len(str(mount.get("target", "")).encode("utf-8"))
-        total += len(str(mount.get("mode", "")).encode("utf-8"))
-        for path, content in mount.get("files", {}).items():
-            total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
-    for path, content in data.get("files", {}).items():
-        total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
-    return total
-
-
-class GitMountItem(BaseModel):
-    remote_url: str = Field(description="Git remote URL (HTTPS or SSH)")
-    source_path: str = Field(default=".", description="Path within repository (supports glob patterns)")
-    target_path: str = Field(description="Absolute path inside container")
-    branch: str | None = Field(default=None, description="Optional branch or tag name")
-
-    @field_validator("remote_url")
-    @classmethod
-    def validate_remote_url(cls, v: str) -> str:
-        if not v.startswith(("http://", "https://", "git@", "ssh://")):
-            raise ValueError("remote_url must be a valid git URL (https://, git@, or ssh://)")
-        return v
-
-    @field_validator("source_path")
-    @classmethod
-    def validate_source_path(cls, v: str) -> str:
-        if v.startswith("/"):
-            raise ValueError("source_path must be relative (no leading /)")
-        if ".." in v:
-            raise ValueError("source_path cannot contain path traversal (..)")
-        return v
-
-    @field_validator("target_path")
-    @classmethod
-    def validate_target_path(cls, v: str) -> str:
-        if ".." in v:
-            raise ValueError("target_path cannot contain path traversal (..)")
-        return v
-
-
-class MountItem(BaseModel):
-    target: str = Field(description="Absolute mount target path")
-    mode: str = Field(default="rw", description="Mount mode: ro or rw")
-    files: dict = Field(default_factory=dict, description="Files as {relative_path: content}")
-
-    @field_validator("target")
-    @classmethod
-    def validate_target(cls, v: str) -> str:
-        if not v.startswith("/"):
-            raise ValueError("Mount target must be absolute (start with /)")
-        return v
-
-    @field_validator("mode")
-    @classmethod
-    def validate_mode(cls, v: str) -> str:
-        if v not in ("ro", "rw"):
-            raise ValueError("Mount mode must be 'ro' or 'rw'")
-        return v
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict) -> dict:
-        for path in v.keys():
-            if ".." in path or not path:
-                raise ValueError(f"Invalid file path: {path}")
-            if path.startswith("/"):
-                raise ValueError(
-                    f"Mount file paths must be relative (got: {path}). "
-                    f"The mount target defines the absolute container path."
-                )
-        return v
-
-
-class ConfigProfileCreate(BaseModel):
-    name: str = Field(description="Profile name (unique per user)")
-    description: str | None = Field(default=None, description="Optional description")
-    project_id: str | None = Field(default=None, description="Optional project ID")
-    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
-    env_vars: dict = Field(default_factory=dict, description="Environment variables")
-    runtime_hints: dict = Field(default_factory=dict, description="Runtime hints")
-    mounts: list[MountItem] = Field(default_factory=list, description="Mount definitions")
-    files: dict = Field(default_factory=dict, description="Files as {relative_path: content}")
-    git_mounts: list[GitMountItem] = Field(default_factory=list, description="Git repository mounts")
-    is_default: bool = Field(default=False, description="Whether this is the default profile for its scope")
-
-    @field_validator("project_id", "tool_type_id")
-    @classmethod
-    def validate_uuids(cls, v: str | None) -> str | None:
-        return _validate_uuid(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict) -> dict:
-        for path in v.keys():
-            if ".." in path or not path:
-                raise ValueError(f"Invalid file path: {path}")
-            if path.startswith("/"):
-                raise ValueError(
-                    f"File paths must be relative (got: {path}). "
-                    f"Use Mounts for absolute container paths."
-                )
-        return v
-
-    @field_validator("env_vars")
-    @classmethod
-    def validate_env_vars(cls, v: dict) -> dict:
-        result = _validate_env_vars(v)
-        if result is None:
-            raise ValueError("env_vars must be a JSON object")
-        return result
-
-    @field_validator("runtime_hints")
-    @classmethod
-    def validate_runtime_hints(cls, v: dict) -> dict:
-        if not isinstance(v, dict):
-            raise ValueError("runtime_hints must be a JSON object")
-        return v
-
-    @field_validator("mounts")
-    @classmethod
-    def validate_mounts(cls, v: list) -> list:
-        if not isinstance(v, list):
-            raise ValueError("mounts must be a JSON array")
-        return v
-
-
-class ConfigProfileUpdate(BaseModel):
-    name: str | None = Field(default=None, description="Profile name")
-    description: str | None = Field(default=None, description="Optional description")
-    project_id: str | None = Field(default=None, description="Optional project ID")
-    tool_type_id: str | None = Field(default=None, description="Optional tool type ID")
-    env_vars: dict | None = Field(default=None, description="Environment variables")
-    runtime_hints: dict | None = Field(default=None, description="Runtime hints")
-    mounts: list[MountItem] | None = Field(default=None, description="Mount definitions")
-    files: dict | None = Field(default=None, description="Files as {relative_path: content}")
-    git_mounts: list[GitMountItem] | None = Field(default=None, description="Git repository mounts")
-    is_default: bool | None = Field(default=None, description="Whether this is the default profile")
-
-    @field_validator("project_id", "tool_type_id")
-    @classmethod
-    def validate_uuids(cls, v: str | None) -> str | None:
-        return _validate_uuid(v)
-
-    @field_validator("files")
-    @classmethod
-    def validate_files(cls, v: dict | None) -> dict | None:
-        if v is None:
-            return v
-        for path in v.keys():
-            if ".." in path or path.startswith("/") or not path:
-                raise ValueError(f"Invalid file path: {path}")
-        return v
-
-
-class ConfigProfileIncludeUpdate(BaseModel):
-    includes: list[str] = Field(description="Ordered list of included profile IDs")
-
-    @field_validator("includes")
-    @classmethod
-    def validate_includes(cls, v: list) -> list:
-        for item in v:
-            try:
-                uuid.UUID(item)
-            except ValueError:
-                raise ValueError(f"Invalid UUID in includes: {item}")
-        return v
-
-
-class ConfigProfileResponse(BaseModel):
-    id: str
-    user_id: str
-    name: str
-    description: str | None
-    project_id: str | None
-    tool_type_id: str | None
-    env_vars: dict
-    runtime_hints: dict
-    mounts: list
-    files: dict
-    git_mounts: list
-    is_default: bool
-    includes: list[dict]
-    created_at: str
-    updated_at: str
-
-
-async def _get_profile_with_includes(session: AsyncSession, profile_id: uuid.UUID) -> ConfigProfile | None:
-    """Fetch a profile with includes eagerly loaded."""
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile_id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    return result.scalar_one_or_none()
-
-
-async def _check_access(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    project_id: uuid.UUID | None = None,
-    tool_type_id: uuid.UUID | None = None,
-) -> None:
-    """Verify user has access to referenced project and tool type."""
-    if project_id is not None:
-        project = await session.get(Project, project_id)
-        if project is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Project not found")
-        # Add ownership check if needed; for now just verify existence
-    if tool_type_id is not None:
-        tool_type = await session.get(ToolType, tool_type_id)
-        if tool_type is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Tool type not found")
-
-
-async def _validate_git_mounts(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    git_mounts: list[dict],
-    project_id: uuid.UUID | None = None,
-) -> None:
-    """Validate git mount URLs.
-    
-    Simply checks that remote_url looks like a valid git URL.
-    Actual clone validation happens at instance startup time.
-    """
-    for mount in git_mounts:
-        remote_url = mount.get("remote_url")
-        if not remote_url:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Git mount missing remote_url",
-            )
-        
-        if not remote_url.startswith(("http://", "https://", "git@", "ssh://")):
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail=f"Invalid git URL: {remote_url}",
-            )
-
-
-def _profile_to_response(profile: ConfigProfile, includes: list[ConfigProfileInclude] | None = None) -> dict:
-    return {
-        "id": str(profile.id),
-        "user_id": str(profile.user_id),
-        "name": profile.name,
-        "description": profile.description,
-        "project_id": str(profile.project_id) if profile.project_id else None,
-        "tool_type_id": str(profile.tool_type_id) if profile.tool_type_id else None,
-        "env_vars": profile.env_vars or {},
-        "runtime_hints": profile.runtime_hints or {},
-        "mounts": profile.mounts or [],
-        "git_mounts": profile.git_mounts or [],
-        "files": profile.files or {},
-        "is_default": profile.is_default,
-        "includes": [
-            {
-                "id": str(inc.id),
-                "included_profile_id": str(inc.included_profile_id),
-                "order_index": inc.order_index,
-            }
-            for inc in (includes or profile.includes)
-        ],
-        "created_at": profile.created_at.isoformat() if profile.created_at else None,
-        "updated_at": profile.updated_at.isoformat() if profile.updated_at else None,
-    }
-
-
-@router.get("", response_model=list[ConfigProfileResponse])
-async def list_config_profiles(
-    project_id: str | None = Query(None, description="Filter by project compatibility"),
-    tool_type_id: str | None = Query(None, description="Filter by tool type compatibility"),
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """List config profiles, optionally filtered by compatibility."""
-    user_uuid = current_user_id
-    query = select(ConfigProfile).where(ConfigProfile.user_id == user_uuid).options(selectinload(ConfigProfile.includes))
-
-    if project_id or tool_type_id:
-        # Compatibility filter: include portable profiles and matching scoped profiles
-        project_uuid = uuid.UUID(project_id) if project_id else None
-        tool_uuid = uuid.UUID(tool_type_id) if tool_type_id else None
-
-        from sqlalchemy import or_
-
-        conditions: list = []
-        # Portable profiles (no project, no tool)
-        conditions.append(
-            (ConfigProfile.project_id.is_(None)) & (ConfigProfile.tool_type_id.is_(None))
-        )
-        if project_uuid:
-            # Profiles matching this project (with or without tool)
-            conditions.append(ConfigProfile.project_id == project_uuid)
-        if tool_uuid:
-            # Profiles matching this tool (with or without project)
-            conditions.append(ConfigProfile.tool_type_id == tool_uuid)
-        if project_uuid and tool_uuid:
-            # Exact match
-            conditions.append(
-                (ConfigProfile.project_id == project_uuid) & (ConfigProfile.tool_type_id == tool_uuid)
-            )
-
-        query = query.where(or_(*conditions))
-
-    result = await session.execute(query)
-    profiles = result.scalars().all()
-    return [_profile_to_response(p) for p in profiles]
-
-
-@router.post("", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED)
-async def create_config_profile(
-    data: ConfigProfileCreate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Create a new config profile."""
-    user_uuid = current_user_id
-
-    # Check for duplicate name
-    existing = await session.execute(
-        select(ConfigProfile).where(
-            ConfigProfile.user_id == user_uuid,
-            ConfigProfile.name == data.name,
-        ).options(selectinload(ConfigProfile.includes))
-    )
-    if existing.scalar_one_or_none() is not None:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"Profile with name '{data.name}' already exists",
-        )
-
-    # Validate references
-    project_uuid = uuid.UUID(data.project_id) if data.project_id else None
-    tool_uuid = uuid.UUID(data.tool_type_id) if data.tool_type_id else None
-    await _check_access(session, user_uuid, project_uuid, tool_uuid)
-    
-    # Validate git mounts reference existing repositories
-    if data.git_mounts:
-        git_mounts_data = [m.model_dump() if hasattr(m, "model_dump") else m for m in data.git_mounts]
-        await _validate_git_mounts(session, user_uuid, git_mounts_data, project_uuid)
-
-    # Check size
-    size = _calculate_profile_size(data.model_dump())
-    if size > MAX_PROFILE_SIZE_BYTES:
-        raise HTTPException(
-            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
-            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
-        )
-
-    profile = ConfigProfile(
-        user_id=user_uuid,
-        name=data.name,
-        description=data.description,
-        project_id=project_uuid,
-        tool_type_id=tool_uuid,
-        env_vars=data.env_vars,
-        runtime_hints=data.runtime_hints,
-        mounts=[m.model_dump() for m in data.mounts],
-        git_mounts=[m.model_dump() for m in data.git_mounts],
-        files=data.files,
-        is_default=data.is_default,
-    )
-    session.add(profile)
-    await session.commit()
-
-    # Re-fetch with includes to avoid lazy loading issues
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile.id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    profile = result.scalar_one()
-
-    logger.debug("Created config profile %s for user %s", profile.id, user_uuid)
-    return _profile_to_response(profile)
-
-
-@router.get("/{profile_id}", response_model=ConfigProfileResponse)
-async def get_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Get a config profile by ID."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-    return _profile_to_response(profile)
-
-
-@router.put("/{profile_id}", response_model=ConfigProfileResponse)
-async def update_config_profile(
-    profile_id: str,
-    data: ConfigProfileUpdate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Update a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-
-    update_data = data.model_dump(exclude_unset=True)
-
-    # Handle name uniqueness
-    if "name" in update_data:
-        existing = await session.execute(
-            select(ConfigProfile).where(
-                ConfigProfile.user_id == profile.user_id,
-                ConfigProfile.name == update_data["name"],
-                ConfigProfile.id != profile.id,
-            )
-        )
-        if existing.scalar_one_or_none() is not None:
-            raise HTTPException(
-                status_code=status.HTTP_409_CONFLICT,
-                detail=f"Profile with name '{update_data['name']}' already exists",
-            )
-
-    # Validate references
-    project_uuid = (
-        uuid.UUID(update_data["project_id"])
-        if "project_id" in update_data and update_data["project_id"]
-        else (profile.project_id if "project_id" not in update_data else None)
-    )
-    tool_uuid = (
-        uuid.UUID(update_data["tool_type_id"])
-        if "tool_type_id" in update_data and update_data["tool_type_id"]
-        else (profile.tool_type_id if "tool_type_id" not in update_data else None)
-    )
-    await _check_access(session, profile.user_id, project_uuid, tool_uuid)
-    
-    # Validate git mounts reference existing repositories
-    if "git_mounts" in update_data and update_data["git_mounts"] is not None:
-        git_mounts_data = [
-            m.model_dump() if hasattr(m, "model_dump") else m 
-            for m in update_data["git_mounts"]
-        ]
-        await _validate_git_mounts(session, profile.user_id, git_mounts_data, project_uuid)
-
-    # Check size
-    current_data = _profile_to_response(profile)
-    merged = {**current_data, **update_data}
-    size = _calculate_profile_size(merged)
-    if size > MAX_PROFILE_SIZE_BYTES:
-        raise HTTPException(
-            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
-            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
-        )
-
-    # Apply updates
-    for field_name, value in update_data.items():
-        if field_name in ("project_id", "tool_type_id"):
-            value = uuid.UUID(value) if value else None
-        elif field_name == "mounts" and value is not None:
-            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
-        elif field_name == "git_mounts" and value is not None:
-            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
-        setattr(profile, field_name, value)
-
-    await session.commit()
-
-    # Re-fetch with includes to avoid lazy loading issues
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile.id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    profile = result.scalar_one()
-
-    logger.debug("Updated config profile %s", profile.id)
-    return _profile_to_response(profile)
-
-
-@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Delete a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-
-    await session.delete(profile)
-    await session.commit()
-
-    logger.debug("Deleted config profile %s", profile_id)
-    return None
-
-
-@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
-async def update_profile_includes(
-    profile_id: str,
-    data: ConfigProfileIncludeUpdate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Update the ordered includes for a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-
-    # Validate all included profiles exist and belong to the user
-    included_uuids = [uuid.UUID(inc_id) for inc_id in data.includes]
-    for inc_uuid in included_uuids:
-        inc_profile = await session.get(ConfigProfile, inc_uuid)
-        if inc_profile is None:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"Included profile not found: {inc_uuid}",
-            )
-        if inc_profile.user_id != current_user_id:
-            raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN,
-                detail=f"Not authorized to include profile: {inc_uuid}",
-            )
-        if inc_uuid == profile.id:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Profile cannot include itself",
-            )
-
-    # Check for cycles
-    cycle = await check_include_cycle(session, profile.id, None)
-    if cycle is None and included_uuids:
-        # Check each new include would not create a cycle
-        for inc_uuid in included_uuids:
-            cycle = await check_include_cycle(session, profile.id, inc_uuid)
-            if cycle is not None:
-                break
-
-    if cycle is not None:
-        cycle_str = " -> ".join(str(c) for c in cycle)
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"Include cycle detected: {cycle_str}",
-        )
-
-    # Remove existing includes
-    result = await session.execute(
-        select(ConfigProfileInclude).where(ConfigProfileInclude.profile_id == profile.id)
-    )
-    for existing in result.scalars().all():
-        await session.delete(existing)
-    await session.flush()
-
-    # Add new includes
-    for order_index, inc_uuid in enumerate(included_uuids):
-        include = ConfigProfileInclude(
-            profile_id=profile.id,
-            included_profile_id=inc_uuid,
-            order_index=order_index,
-        )
-        session.add(include)
-    await session.flush()
-
-    await session.commit()
-
-    # Re-fetch profile (includes loaded separately due to SQLite async issue)
-    result = await session.execute(
-        select(ConfigProfile).where(ConfigProfile.id == profile.id)
-    )
-    profile = result.scalar_one()
-
-    inc_result = await session.execute(
-        select(ConfigProfileInclude).where(ConfigProfileInclude.profile_id == profile.id)
-    )
-    direct_includes = inc_result.scalars().all()
-
-    logger.debug("Updated includes for config profile %s", profile.id)
-    return _profile_to_response(profile, list(direct_includes))
-
-
-@router.get("/{profile_id}/preview")
-async def preview_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Preview the resolved output of a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found")
-    if profile.user_id != current_user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized")
-
-    try:
-        resolved = await resolve_profile(session, profile.id)
-    except ConfigProfileCycleError as exc:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=str(exc),
-        )
-
-    return resolved_profile_to_dict(resolved)
-
-
-@router.get("/defaults/resolve")
-async def resolve_default_profile(
-    project_id: str = Query(..., description="Project ID"),
-    tool_type_id: str = Query(..., description="Tool type ID"),
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Resolve the default config profile for a project/tool combination.
-
-    Selects by specificity:
-    1. project+tool explicit default
-    2. project explicit default
-    3. tool explicit default
-    4. global/user explicit default
-    5. first created compatible profile
-    6. none (returns null)
-    """
-    user_uuid = current_user_id
-    project_uuid = uuid.UUID(project_id)
-    tool_uuid = uuid.UUID(tool_type_id)
-
-    # Fetch all compatible profiles ordered by created_at
-    query = (
-        select(ConfigProfile)
-        .where(ConfigProfile.user_id == user_uuid)
-        .where(
-            (ConfigProfile.project_id.is_(None) & ConfigProfile.tool_type_id.is_(None))
-            | (ConfigProfile.project_id == project_uuid)
-            | (ConfigProfile.tool_type_id == tool_uuid)
-            | (
-                (ConfigProfile.project_id == project_uuid)
-                & (ConfigProfile.tool_type_id == tool_uuid)
-            )
-        )
-        .order_by(ConfigProfile.created_at)
-    )
-    result = await session.execute(query)
-    profiles = result.scalars().all()
-
-    if not profiles:
-        return {"profile_id": None, "profile_name": None}
-
-    # Check explicit defaults by specificity
-    explicit_defaults = [p for p in profiles if p.is_default]
-
-    # Most specific: project+tool
-    for p in explicit_defaults:
-        if p.project_id == project_uuid and p.tool_type_id == tool_uuid:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Next: project only
-    for p in explicit_defaults:
-        if p.project_id == project_uuid and p.tool_type_id is None:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Next: tool only
-    for p in explicit_defaults:
-        if p.project_id is None and p.tool_type_id == tool_uuid:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Next: global/user (no project, no tool)
-    for p in explicit_defaults:
-        if p.project_id is None and p.tool_type_id is None:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Fall back to first created compatible profile
-    first = profiles[0]
-    return {"profile_id": str(first.id), "profile_name": first.name}

apps/api/src/api/project/.pi-map.index.md

@@ -0,0 +1,22 @@
+# apps/api/src/api/project (index)
+dir: apps/api/src/api/project
+
+## role
+Provides FastAPI REST API endpoints for project and Git repository management, exposing CRUD operations and version control functionality to API consumers.
+## parent
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- git_repositories.py
+- projects.py
+## links
+index: apps/api/src/api/project/.pi-map.index.md
+map: apps/api/src/api/project/.pi-map.md
+## workflows
+- change project behavior
+  read: __init__.py, git_repositories.py, projects.py
+## dirty
+-

apps/api/src/api/project/__init__.py

@@ -0,0 +1,6 @@
+"""Project API routers module."""
+
+from src.api.project.git_repositories import router as git_repositories_router
+from src.api.project.projects import router as projects_router
+
+__all__ = ["git_repositories_router", "projects_router"]

apps/api/src/api/project/git_repositories.py

@@ -0,0 +1,500 @@
+import logging
+import os
+import shutil
+import uuid
+from fastapi import APIRouter, Depends, HTTPException, Response, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import (
+    _get_owned_project,
+    _get_user,
+    get_current_user_id,
+    get_db_session,
+)
+from src.models import GitRepository, SSHKey
+from src.schemas.project.git_repository import (
+    BranchCreateRequest,
+    BranchesResponse,
+    CheckoutRequest,
+    CommitRequest,
+    CommitResponse,
+    FetchResponse,
+    FileContentResponse,
+    FileListResponse,
+    FileUpdateRequest,
+    FileUpdateResponse,
+    GitRepositoryCreate,
+    GitRepositoryResponse,
+    MergeRequest,
+    MergeResponse,
+    PullResponse,
+    PushResponse,
+    StatusResponse,
+    UpdateSSHKeyRequest,
+    URLParseRequest,
+    URLParseResponse,
+)
+from src.services.git.operations import (
+    clone_working_repository,
+    get_repo_path,
+    init_working_repository,
+    list_remote_branches,
+    preflight_remote_repository,
+)
+from src.utils.git_control import (
+    checkout_branch,
+    commit_changes,
+    create_branch,
+    delete_branch,
+    fetch,
+    get_status,
+    merge,
+    pull,
+    push,
+)
+from src.utils.git_files import commit_file, get_file_content, list_branches, list_tree
+from src.utils.git_history import get_commit_detail, get_commit_history
+from src.utils.git_url_parser import parse_git_url
+
+router = APIRouter(prefix="/projects", tags=["git-repositories"])
+logger = logging.getLogger(__name__)
+
+
+async def _get_repo(
+    session: AsyncSession, user_id: uuid.UUID, project_id: uuid.UUID, repo_id: uuid.UUID
+) -> GitRepository:
+    _user = await _get_user(session, user_id)
+    _project = await _get_owned_project(project_id, user_id, session)
+    repo = await session.get(GitRepository, repo_id)
+    if repo is None or repo.project_id != project_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found")
+    return repo
+
+
+async def _get_repo_on_disk(
+    session: AsyncSession, user_id: uuid.UUID, project_id: uuid.UUID, repo_id: uuid.UUID
+) -> GitRepository:
+    repo = await _get_repo(session, user_id, project_id, repo_id)
+    if not os.path.exists(repo.path):
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk")
+    return repo
+
+
+def _parse_remote_url(remote_url: str | None, force_original: bool) -> str | None:
+    if not remote_url or force_original:
+        return remote_url
+    parse_result = parse_git_url(remote_url)
+    if parse_result["needs_parsing"] and parse_result["base_url"]:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail={
+                "message": "The provided URL appears to be a browser URL, not a git clone URL",
+                "suggested_url": parse_result["base_url"],
+                "original_url": remote_url,
+                "error_code": "URL_NEEDS_PARSING",
+            },
+        )
+    return parse_result.get("base_url") or remote_url
+
+
+async def _commit_author(session: AsyncSession, user_id: uuid.UUID) -> tuple[str, str]:
+    user = await _get_user(session, user_id)
+    return user.name or "Unknown", user.email or "unknown@example.com"
+
+
+@router.get("/repositories", response_model=list[GitRepositoryResponse])
+async def list_user_repositories(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> list[GitRepository]:
+    """List all repositories owned by the user."""
+    result = await session.execute(select(GitRepository).where(GitRepository.owner_id == user_id))
+    return list(result.scalars().all())
+
+
+@router.post("/repositories/parse-url", response_model=URLParseResponse)
+async def parse_repository_url(data: URLParseRequest) -> URLParseResponse:
+    """Parse a git URL and detect if it's a browser URL that needs correction."""
+    return URLParseResponse(**parse_git_url(data.url))
+
+
+@router.post("/repositories", response_model=GitRepositoryResponse, status_code=status.HTTP_201_CREATED)
+async def create_external_repository(
+    data: GitRepositoryCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> GitRepository:
+    """Create a new external git repository (not tied to any project)."""
+    _user = await _get_user(session, user_id)
+    existing = await session.execute(
+        select(GitRepository).where(
+            GitRepository.project_id.is_(None),
+            GitRepository.owner_id == user_id,
+            GitRepository.name == data.name,
+        )
+    )
+    if existing.scalar_one_or_none():
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="repository name already exists")
+    remote_url = _parse_remote_url(data.remote_url, data.force_original_url)
+    ssh_key_id, ssh_key = None, None
+    if data.ssh_key_id:
+        try:
+            ssh_key_id = uuid.UUID(data.ssh_key_id)
+        except ValueError:
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
+        ssh_key = await session.get(SSHKey, ssh_key_id)
+        if ssh_key is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        if ssh_key.user_id != user_id:
+            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user")
+    if remote_url:
+        preflight_remote_repository(remote_url, ssh_key)
+    repo = GitRepository(name=data.name, path="", project_id=None, owner_id=user_id, remote_url=remote_url, ssh_key_id=ssh_key_id)
+    session.add(repo)
+    await session.flush()
+    repo_path = f"/data/repos/external/{user_id}/{repo.id}"
+    repo.path = repo_path
+    if remote_url:
+        try:
+            clone_working_repository(remote_url, repo_path, ssh_key)
+            repo.is_mirror = False
+        except Exception as exc:
+            await session.rollback()
+            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=f"Failed to clone repository: {exc}")
+    else:
+        init_working_repository(repo_path)
+        repo.is_mirror = False
+    await session.commit()
+    return repo
+
+
+@router.get("/{project_id}/repositories", response_model=list[GitRepositoryResponse])
+async def list_repositories(
+    project_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> list[GitRepository]:
+    _user = await _get_user(session, user_id)
+    _project = await _get_owned_project(project_id, user_id, session)
+    result = await session.execute(select(GitRepository).where(GitRepository.project_id == project_id))
+    return list(result.scalars().all())
+
+
+@router.delete("/{project_id}/repositories/{repo_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_repository(
+    project_id: uuid.UUID, repo_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> Response:
+    repo = await _get_repo(session, user_id, project_id, repo_id)
+    if os.path.exists(repo.path):
+        shutil.rmtree(repo.path)
+    await session.delete(repo)
+    await session.commit()
+    return Response(status_code=status.HTTP_204_NO_CONTENT)
+
+
+@router.post("/{project_id}/repositories", response_model=GitRepositoryResponse, status_code=status.HTTP_201_CREATED)
+async def create_repository(
+    project_id: uuid.UUID,
+    data: GitRepositoryCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> GitRepository:
+    """Create a new git repository in a project."""
+    _user = await _get_user(session, user_id)
+    _project = await _get_owned_project(project_id, user_id, session)
+    existing = await session.execute(
+        select(GitRepository).where(GitRepository.project_id == project_id, GitRepository.name == data.name)
+    )
+    if existing.scalar_one_or_none():
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="repository name already exists")
+    remote_url = _parse_remote_url(data.remote_url, data.force_original_url)
+    ssh_key_id, ssh_key = None, None
+    if data.ssh_key_id:
+        try:
+            ssh_key_id = uuid.UUID(data.ssh_key_id)
+        except ValueError:
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
+        ssh_key = await session.get(SSHKey, ssh_key_id)
+        if ssh_key is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        if ssh_key.user_id != user_id and ssh_key.project_id != project_id:
+            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user or project")
+    if remote_url:
+        preflight_remote_repository(remote_url, ssh_key)
+    repo_path = get_repo_path(user_id, project_id, data.name)
+    os.makedirs(os.path.dirname(repo_path), exist_ok=True)
+    if remote_url:
+        clone_working_repository(remote_url, repo_path, ssh_key)
+    else:
+        init_working_repository(repo_path)
+    repo = GitRepository(
+        name=data.name, path=repo_path, project_id=project_id, owner_id=user_id,
+        is_mirror=False, remote_url=remote_url, ssh_key_id=ssh_key_id,
+    )
+    session.add(repo)
+    await session.commit()
+    await session.refresh(repo)
+    return repo
+
+
+@router.patch("/{project_id}/repositories/{repo_id}/ssh-key", response_model=GitRepositoryResponse)
+async def update_repository_ssh_key(
+    project_id: uuid.UUID, repo_id: uuid.UUID, data: UpdateSSHKeyRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> GitRepository:
+    repo = await _get_repo(session, user_id, project_id, repo_id)
+    if data.ssh_key_id:
+        try:
+            ssh_key_id = uuid.UUID(data.ssh_key_id)
+        except ValueError:
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid ssh_key_id format")
+        ssh_key = await session.get(SSHKey, ssh_key_id)
+        if ssh_key is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        if ssh_key.user_id != user_id and ssh_key.project_id != project_id:
+            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="ssh key does not belong to user or project")
+        repo.ssh_key_id = ssh_key_id
+    else:
+        repo.ssh_key_id = None
+    await session.commit()
+    await session.refresh(repo)
+    return repo
+
+
+@router.get("/{project_id}/repositories/{repo_id}/history")
+async def get_repository_history(
+    project_id: uuid.UUID, repo_id: uuid.UUID,
+    view: str = "graph", branch: str | None = None, limit: int = 100, offset: int = 0,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        return get_commit_history(repo.path, branch=branch, limit=limit, offset=offset)
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(e))
+
+
+@router.get("/{project_id}/repositories/{repo_id}/commits/{commit_hash}")
+async def get_repository_commit(
+    project_id: uuid.UUID, repo_id: uuid.UUID, commit_hash: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        return get_commit_detail(repo.path, commit_hash)
+    except (RuntimeError, ValueError) as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.get("/{project_id}/repositories/{repo_id}/files", response_model=FileListResponse)
+async def list_repository_files(
+    project_id: uuid.UUID, repo_id: uuid.UUID, branch: str = "main", path: str = "",
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> FileListResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        entries = list_tree(repo.path, branch=branch, path=path)
+        return FileListResponse(path=path, branch=branch, entries=[
+            {"name": e.name, "type": e.type, "path": e.path, "size": e.size, "mode": e.mode, "last_commit": e.last_commit}
+            for e in entries
+        ])
+    except RuntimeError as e:
+        logger.error("Failed to list files for repo %s: %s", repo_id, str(e))
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.get("/{project_id}/repositories/{repo_id}/files/content", response_model=FileContentResponse)
+async def get_repository_file_content(
+    project_id: uuid.UUID, repo_id: uuid.UUID, branch: str, path: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> FileContentResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        fc = get_file_content(repo.path, branch=branch, path=path)
+        return FileContentResponse(path=fc.path, branch=fc.branch, content=fc.content, size=fc.size,
+            encoding=fc.encoding, language=fc.language, is_binary=fc.is_binary, last_commit=fc.last_commit)
+    except FileNotFoundError:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="file not found")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.get("/{project_id}/repositories/{repo_id}/branches", response_model=BranchesResponse)
+async def get_repository_branches(
+    project_id: uuid.UUID, repo_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> BranchesResponse:
+    repo = await _get_repo(session, user_id, project_id, repo_id)
+    is_valid = os.path.isdir(os.path.join(repo.path, ".git")) or os.path.isfile(os.path.join(repo.path, "HEAD"))
+    if is_valid:
+        try:
+            branches, default_branch = list_branches(repo.path)
+            return BranchesResponse(branches=[
+                {"name": b.name, "is_default": b.is_default, "last_commit": b.last_commit} for b in branches
+            ], default_branch=default_branch)
+        except RuntimeError as e:
+            logger.error("Failed to list branches for repo %s: %s", repo_id, str(e))
+            raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(e)) from e
+    if repo.remote_url:
+        ssh_key = await session.get(SSHKey, repo.ssh_key_id) if repo.ssh_key_id else None
+        try:
+            remote_branches, default_branch = list_remote_branches(repo.remote_url, ssh_key)
+            if remote_branches:
+                return BranchesResponse(branches=[
+                    {"name": b, "is_default": b == default_branch, "last_commit": None} for b in remote_branches
+                ], default_branch=default_branch)
+        except RuntimeError:
+            pass
+    raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="repository not found on disk — re-clone or re-create the repository")
+
+
+@router.post("/{project_id}/repositories/{repo_id}/files/content", response_model=FileUpdateResponse)
+async def update_repository_file(
+    project_id: uuid.UUID, repo_id: uuid.UUID, data: FileUpdateRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> FileUpdateResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    author_name, author_email = await _commit_author(session, user_id)
+    try:
+        commit_hash = commit_file(repo.path, data.branch, data.path, data.content, data.commit_message, author_name, author_email)
+        return FileUpdateResponse(commit_hash=commit_hash, message=data.commit_message, branch=data.branch)
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.get("/{project_id}/repositories/{repo_id}/status", response_model=StatusResponse)
+async def get_repository_status(
+    project_id: uuid.UUID, repo_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> StatusResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        s = get_status(repo.path)
+        return StatusResponse(branch=s.branch, modified=s.modified, added=s.added, deleted=s.deleted,
+            untracked=s.untracked, renamed=s.renamed, ahead=s.ahead, behind=s.behind)
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.post("/{project_id}/repositories/{repo_id}/branches")
+async def create_repository_branch(
+    project_id: uuid.UUID, repo_id: uuid.UUID, data: BranchCreateRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        create_branch(repo.path, data.name, data.base_branch)
+        return {"message": f"Branch '{data.name}' created", "branch": data.name}
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.delete("/{project_id}/repositories/{repo_id}/branches/{branch_name}")
+async def delete_repository_branch(
+    project_id: uuid.UUID, repo_id: uuid.UUID, branch_name: str, force: bool = False,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        delete_branch(repo.path, branch_name, force)
+        return {"message": f"Branch '{branch_name}' deleted"}
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.post("/{project_id}/repositories/{repo_id}/checkout")
+async def checkout_repository_branch(
+    project_id: uuid.UUID, repo_id: uuid.UUID, data: CheckoutRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        checkout_branch(repo.path, data.branch)
+        return {"message": f"Checked out branch '{data.branch}'", "branch": data.branch}
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.post("/{project_id}/repositories/{repo_id}/commit", response_model=CommitResponse)
+async def commit_repository_changes(
+    project_id: uuid.UUID, repo_id: uuid.UUID, data: CommitRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> CommitResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    author_name, author_email = await _commit_author(session, user_id)
+    try:
+        commit_hash = commit_changes(repo.path, data.message, author_name, author_email, data.files)
+        return CommitResponse(commit_hash=commit_hash, message=data.message)
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.post("/{project_id}/repositories/{repo_id}/fetch", response_model=FetchResponse)
+async def fetch_repository(
+    project_id: uuid.UUID, repo_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> FetchResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        fetch(repo.path)
+        return FetchResponse(message="Fetched from remote")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.post("/{project_id}/repositories/{repo_id}/pull", response_model=PullResponse)
+async def pull_repository(
+    project_id: uuid.UUID, repo_id: uuid.UUID, branch: str | None = None,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> PullResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        pull(repo.path, branch)
+        return PullResponse(message="Pulled from remote")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.post("/{project_id}/repositories/{repo_id}/push", response_model=PushResponse)
+async def push_repository(
+    project_id: uuid.UUID, repo_id: uuid.UUID, branch: str | None = None,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> PushResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        push(repo.path, branch)
+        return PushResponse(message="Pushed to remote")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
+
+
+@router.post("/{project_id}/repositories/{repo_id}/merge", response_model=MergeResponse)
+async def merge_repository_branches(
+    project_id: uuid.UUID, repo_id: uuid.UUID, data: MergeRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> MergeResponse:
+    repo = await _get_repo_on_disk(session, user_id, project_id, repo_id)
+    try:
+        commit_hash = merge(repo.path, data.source_branch, data.target_branch, data.message)
+        return MergeResponse(commit_hash=commit_hash, message=data.message or f"Merge {data.source_branch}")
+    except RuntimeError as e:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))

apps/api/src/api/project/projects.py

@@ -3,42 +3,29 @@ import shutil
 import uuid
 
 from fastapi import APIRouter, Depends, HTTPException, Response, status
-from pydantic import BaseModel, ConfigDict
-from sqlalchemy import select
+from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession
 
-from src.auth.dependencies import _get_owned_project, _get_user, get_current_user_id, get_db_session
-from src.models.git_repository import GitRepository
+from src.auth.dependencies import (
+    _get_owned_project,
+    _get_user,
+    get_current_user_id,
+    get_db_session,
+)
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
+from src.models import ToolInstance
+from src.schemas.project import (
+    ProjectCreate,
+    ProjectResponse,
+    ProjectUpdate,
+    SetDefaultSSHKeyRequest,
+)
 
 router = APIRouter(prefix="/projects", tags=["projects"])
 
 
-class ProjectCreate(BaseModel):
-    name: str
-    description: str | None = None
-
-
-class ProjectUpdate(BaseModel):
-    name: str | None = None
-    description: str | None = None
-
-
-class ProjectResponse(BaseModel):
-    model_config = ConfigDict(from_attributes=True)
-
-    id: uuid.UUID
-    name: str
-    description: str | None
-    owner_id: uuid.UUID
-    default_ssh_key_id: uuid.UUID | None
-
-
-class SetDefaultSSHKeyRequest(BaseModel):
-    ssh_key_id: uuid.UUID
-
-
 @router.post(
     "",
     response_model=ProjectResponse,
@@ -76,26 +63,77 @@ async def create_project(
 
 @router.get(
     "",
-    response_model=list[ProjectResponse],
     summary="List all projects",
-    description="Retrieve all projects owned by the authenticated user.",
+    description="Retrieve all projects owned by the authenticated user with repositories and workspaces.",
 )
 async def list_projects(
     user_id: uuid.UUID = Depends(get_current_user_id),
     session: AsyncSession = Depends(get_db_session),
-) -> list[Project]:
+) -> list[dict]:
     """List all projects for the authenticated user.
 
-    Args:
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        List of projects owned by the user.
+    Returns projects with nested repositories and workspaces for inline display.
     """
     user = await _get_user(session, user_id)
-    result = await session.execute(select(Project).where(Project.owner_id == user.id))
-    return list(result.scalars().all())
+    result = await session.execute(
+        select(Project)
+        .where(Project.owner_id == user.id)
+        .order_by(Project.created_at.desc())
+    )
+    projects = result.scalars().all()
+
+    from src.models import Workspace
+
+    enriched = []
+    for project in projects:
+        repos_result = await session.execute(
+            select(GitRepository).where(GitRepository.project_id == project.id)
+        )
+        repositories = []
+        for repo in repos_result.scalars().all():
+            ws_result = await session.execute(
+                select(Workspace).where(Workspace.repo_id == repo.id)
+            )
+            workspaces = []
+            for ws in ws_result.scalars().all():
+                # Count instances
+                inst_result = await session.execute(
+                    select(func.count()).where(ToolInstance.workspace_id == ws.id)
+                )
+                instance_count = inst_result.scalar() or 0
+                workspaces.append(
+                    {
+                        "id": str(ws.id),
+                        "name": ws.name,
+                        "branch": ws.branch,
+                        "status": ws.status,
+                        "instance_count": instance_count,
+                    }
+                )
+
+            repositories.append(
+                {
+                    "id": str(repo.id),
+                    "name": repo.name,
+                    "remote_url": repo.remote_url,
+                    "workspaces": workspaces,
+                }
+            )
+
+        enriched.append(
+            {
+                "id": str(project.id),
+                "name": project.name,
+                "description": project.description,
+                "owner_id": str(project.owner_id),
+                "repositories": repositories,
+                "created_at": project.created_at.isoformat()
+                if project.created_at
+                else None,
+            }
+        )
+
+    return enriched
 
 
 @router.get(
@@ -184,7 +222,9 @@ async def delete_project(
     project = await _get_owned_project(project_id, user_id, session)
 
     # Delete repositories from disk and database
-    result = await session.execute(select(GitRepository).where(GitRepository.project_id == project_id))
+    result = await session.execute(
+        select(GitRepository).where(GitRepository.project_id == project_id)
+    )
     repositories = result.scalars().all()
     for repo in repositories:
         if os.path.exists(repo.path):

apps/api/src/api/system/.pi-map.index.md

@@ -0,0 +1,30 @@
+# apps/api/src/api/system (index)
+dir: apps/api/src/api/system
+
+## role
+Provides system-level API endpoints for monitoring, administration, and infrastructure operations including dashboards, health checks, event streaming, instance proxying, notifications, and terminal access.
+## parent
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## children
+- apps/api/src/api/system/.ruff_cache
+  index: apps/api/src/api/system/.ruff_cache/.pi-map.index.md
+  map: apps/api/src/api/system/.ruff_cache/.pi-map.md
+## files
+- __init__.py
+- dashboard.py
+- events.py
+- health.py
+- instance_proxy.py
+- notifications.py
+- terminal.py
+## links
+index: apps/api/src/api/system/.pi-map.index.md
+map: apps/api/src/api/system/.pi-map.md
+## workflows
+- change system behavior
+  read: __init__.py, dashboard.py, events.py
+- explore system subdirectories
+  index: apps/api/src/api/system/.ruff_cache/.pi-map.index.md
+## dirty
+-

apps/api/src/api/system/.pi-map.md

@@ -0,0 +1,35 @@
+# apps/api/src/api/system
+dir: apps/api/src/api/system
+
+index: apps/api/src/api/system/.pi-map.index.md
+
+## role
+Provides system-level API endpoints for monitoring, administration, and infrastructure operations including dashboards, health checks, event streaming, instance proxying, notifications, and terminal access.
+## files
+- __init__.py | Aggregates and exports system API routers for a modular web application framework. | dep: src.api.system.dashboard, src.api.system.events, src.api.system.health, src.api.system.instance_proxy, src.api.system.notifications, src.api.system.terminal
+- dashboard.py | Provides a FastAPI endpoint that returns a dashboard summary with counts of projects, repositories, SSH keys, and recent activity for the authenticated user. | exp: func:get_dashboard_summary(user_id, session) → dict, call:session.execute, call:select(func.count()).select_from(Project).where, call:func.count, call:projects_result.scalar, call:select(func.count()).select_from(GitRepository).where, call:repos_result.scalar, call:select(func.count()).select_from(SSHKey).where, call:ssh_keys_result.scalar, call:select(Project) .where(Project.owner_id == user_id) .order_by(Project.created_at.desc()) .limit, call:Project.created_at.desc, call:recent_projects.scalars().all | dep: uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.models.project
+- events.py | Implements an SSE streaming endpoint that delivers instance events to authenticated users with per-user connection limits and heartbeat pings. | dep: asyncio, contextlib, json, uuid, collections.abc, fastapi, src.auth.dependencies, src.services.instance.event_bus
+- health.py | Provides FastAPI health check endpoints that monitor system health including database connectivity/response time and disk usage, returning structured health status responses. | exp: func:health_check() → dict[str, Any], call:HealthChecks, call:time_module.perf_counter, call:SessionLocal, call:session.execute, call:text, call:DatabaseHealth, call:round, call:shutil.disk_usage, call:DiskHealth, call:HealthResponse( status=overall_status, timestamp=datetime.now(timezone.utc).isoformat().replace("+00:00", "Z"), version="0.1.0", checks=checks, uptime_seconds=round(time.time() - _start_time, 2), ).model_dump, call:datetime.now(timezone.utc).isoformat().replace, call:time.time, func:health_check_db() → dict[str, Any], call:time_module.perf_counter, call:SessionLocal, call:session.execute, call:text, call:DatabaseHealthResponse( status="healthy", response_time_ms=round(db_time, 2), ).model_dump, call:round, call:DatabaseHealthResponse( status="unhealthy", response_time_ms=0.0, ).model_dump | dep: time, datetime, typing, fastapi, sqlalchemy, src.database, src.schemas.system, shutil
+- instance_proxy.py | Proxies HTTP requests from authenticated users to running containerized tool instances after verifying ownership and instance status. | exp: func:_proxy_request(request: Request, instance_id: uuid.UUID, path: str, user_id: uuid.UUID, session: AsyncSession) → Response, call:session.get, call:str, call:request.headers.items, call:key.lower, call:httpx.AsyncClient, call:request.body, call:client.request, call:logger.error, call:dict, call:response_headers.pop, call:Response, raise:HTTPException, func:proxy_to_instance(request: Request, instance_id: uuid.UUID, path, user_id, session) → Response, call:_proxy_request | dep: logging, uuid, httpx, fastapi, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models
+- notifications.py | Defines FastAPI REST endpoints for user notification management including listing, marking as read, dismissing, and retrieving unread counts with support for muted categories. | exp: class:NotificationItem, class:NotificationListResponse, class:UnreadCountResponse, class:MarkAllReadResponse, class:ClearAllResponse, func:_get_mute_categories(session: AsyncSession, user_id: uuid.UUID) → list[str], call:session.execute, call:select(UserConfig).where, call:result.scalar_one_or_none, call:config.config.get, call:isinstance, func:list_notifications(limit, offset, unread_only, user, session) → NotificationListResponse, call:_get_mute_categories, call:notification_service.list_notifications, call:NotificationListResponse, call:NotificationItem.model_validate, func:get_unread_count(user, session) → UnreadCountResponse, call:notification_service.get_unread_count, call:UnreadCountResponse, func:mark_notification_read(notification_id: uuid.UUID, user, session) → NotificationItem, call:notification_service.mark_read, call:NotificationItem.model_validate, raise:HTTPException, func:mark_all_read(user, session) → MarkAllReadResponse, call:notification_service.mark_all_read, call:MarkAllReadResponse, func:clear_all_notifications(user, session) → ClearAllResponse, call:notification_service.dismiss_all, call:ClearAllResponse, func:dismiss_notification(notification_id: uuid.UUID, user, session) → None, call:notification_service.dismiss, raise:HTTPException | dep: uuid, datetime, fastapi, pydantic, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models.user, src.models, src.services.shared.notification_service, sqlalchemy
+- terminal.py | Provides WebSocket endpoints for browser-based terminal access to running Docker container tool instances, handling authentication, session management, input/output streaming, and terminal resize/reset operations. | exp: class:SessionRef, method:__init__(self, session, slot_session_id), func:terminal_websocket_default(websocket: WebSocket, instance_id: str, db_session) → None, call:_handle_terminal_websocket, func:terminal_websocket_specific(websocket: WebSocket, instance_id: str, session_id: str, db_session) → None, call:_handle_terminal_websocket, func:_resolve_container_user(db_session: AsyncSession, instance: ToolInstance) → str | None, call:db_session.get, call:dict, call:resolve_base, call:deep_merge, call:get_manifest_container_user, func:_handle_terminal_websocket(websocket: WebSocket, instance_id: str, target_session_id: str | None, db_session: AsyncSession) → None, call:logger.debug, call:websocket.accept, call:uuid.UUID, call:logger.error, call:websocket.close, call:_get_user_from_websocket, call:logger.warning, call:db_session.get, call:get_container_status, call:_resolve_container_user, call:terminal_manager.get_or_create_session, call:terminal_manager.get_session, call:logger.info, call:terminal_manager.create_session, call:terminal_manager._find_key_by_internal_id, call:terminal_manager.attach_websocket, call:websocket.send_json, call:SessionRef, call:asyncio.create_task, call:_write_loop, call:_heartbeat_loop, call:asyncio.wait, call:len, call:task.cancel, call:str, call:suppress, call:terminal_manager.detach_websocket, func:_write_loop(session_ref: SessionRef, websocket, instance_id: str) → None, call:session.is_alive, call:asyncio.sleep, call:websocket.receive, call:session.write_input, call:text.startswith, call:json.loads, call:ctrl.get, call:logger.debug, call:session.resize, call:session.acknowledge_data, call:websocket.send_json, call:terminal_manager.reset_session, call:terminal_manager.attach_websocket, call:text.encode, func:_heartbeat_loop(websocket: WebSocket) → None, call:asyncio.sleep, call:websocket.send_json, func:_get_terminal_instance(instance_id: uuid.UUID, user_id: uuid.UUID, db_session: AsyncSession) → ToolInstance, call:db_session.get, raise:HTTPException, func:list_terminal_sessions(instance_id: uuid.UUID, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.execute, call:select(TerminalSessionModel) .where(TerminalSessionModel.instance_id == instance_id) .where(TerminalSessionModel.status != "closed") .order_by, call:TerminalSessionModel.created_at.asc, call:result.scalars().all, call:terminal_manager.get_session, call:str, call:sessions.append, call:live_session.has_websockets, call:row.created_at.isoformat, call:row.last_activity_at.isoformat, func:create_terminal_session(instance_id: uuid.UUID, data: dict, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.get, call:data.get, call:_resolve_container_user, call:terminal_manager.create_session, raise:HTTPException, func:close_terminal_session(instance_id: uuid.UUID, session_id: str, user_id, db_session) → dict, call:_get_terminal_instance, call:terminal_manager._find_key_by_internal_id, call:str, call:terminal_manager.get_session, call:terminal_manager.close_session, raise:HTTPException, func:reset_specific_terminal_session(instance_id: uuid.UUID, session_id: str, user_id, db_session) → dict, call:_get_terminal_instance, call:terminal_manager._find_key_by_internal_id, call:str, call:terminal_manager.get_session, call:db_session.get, call:_resolve_container_user, call:terminal_manager.reset_session, raise:HTTPException, func:rename_terminal_session(instance_id: uuid.UUID, session_id: str, data: dict, user_id, db_session) → dict, call:_get_terminal_instance, call:data.get, call:isinstance, call:terminal_manager.get_session, call:str, call:db_session.get, call:uuid.UUID, call:db_session.commit, raise:HTTPException, func:reset_terminal_session(instance_id: uuid.UUID, user_id, db_session) → dict, call:_get_terminal_instance, call:db_session.get, call:_resolve_container_user, call:terminal_manager.reset_session, call:logger.info, call:str, call:logger.error, raise:HTTPException, func:_get_user_from_websocket(websocket: WebSocket, db_session: AsyncSession) → uuid.UUID | None, call:websocket.cookies.get, call:Settings, call:decode_session_cookie, call:uuid.UUID, call:str | dep: asyncio, json, logging, uuid, contextlib, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, starlette.websockets, src.auth.dependencies, src.models, src.services.build.manifest_compiler, src.services.terminal.terminal_manager, src.services.docker, src.auth.session, src.config, starlette
+## arch
+Modular FastAPI router pattern with per-feature separation, combining standard REST endpoints, SSE streaming, and WebSocket connections, all with unified authentication and user-scoped access control.
+## tags
+terminal, session, call:terminal, call:, src, get, response, instance
+## symbols
+- NotificationItem
+- NotificationListResponse
+- UnreadCountResponse
+- MarkAllReadResponse
+- ClearAllResponse
+- SessionRef
+- get_dashboard_summary
+- health_check
+## workflows
+- change system behavior
+  read: __init__.py, dashboard.py, events.py
+- explore system subdirectories
+  index: apps/api/src/api/system/.ruff_cache/.pi-map.index.md
+## dirty
+-

apps/api/src/api/system/__init__.py

@@ -0,0 +1,17 @@
+"""System API routers module."""
+
+from src.api.system.dashboard import router as dashboard_router
+from src.api.system.events import router as events_router
+from src.api.system.health import router as health_router
+from src.api.system.instance_proxy import router as instance_proxy_router
+from src.api.system.notifications import router as notifications_router
+from src.api.system.terminal import router as terminal_router
+
+__all__ = [
+    "dashboard_router",
+    "events_router",
+    "health_router",
+    "instance_proxy_router",
+    "notifications_router",
+    "terminal_router",
+]

apps/api/src/api/system/dashboard.py

@@ -5,9 +5,9 @@ from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
 
 router = APIRouter(prefix="/dashboard", tags=["dashboard"])
 

apps/api/src/api/system/events.py

@@ -0,0 +1,80 @@
+"""SSE streaming endpoint for instance events."""
+
+import asyncio
+import contextlib
+import json
+import uuid
+from collections.abc import AsyncGenerator
+
+from fastapi import APIRouter, Depends, HTTPException, Request, status
+from fastapi.responses import StreamingResponse
+
+from src.auth.dependencies import get_current_user_id
+from src.services.instance.event_bus import InstanceEventBus, InstanceEventPayload
+
+router = APIRouter(prefix="/events", tags=["events"])
+
+# In-memory connection counter per user (single-process assumption)
+_connection_counts: dict[uuid.UUID, int] = {}
+MAX_CONNECTIONS_PER_USER = 20
+
+
+@router.get("/stream")
+async def events_stream(
+    request: Request,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+) -> StreamingResponse:
+    """Stream instance events via Server-Sent Events.
+
+    Enforces a maximum of 5 concurrent connections per user.
+    """
+    current = _connection_counts.get(user_id, 0)
+    if current >= MAX_CONNECTIONS_PER_USER:
+        raise HTTPException(
+            status_code=status.HTTP_429_TOO_MANY_REQUESTS,
+            detail="Too many SSE connections",
+        )
+
+    _connection_counts[user_id] = current + 1
+
+    async def event_generator() -> AsyncGenerator[str, None]:
+        event_bus = InstanceEventBus()
+        queue: asyncio.Queue[InstanceEventPayload] = asyncio.Queue(maxsize=100)
+
+        async def on_event(payload: InstanceEventPayload) -> None:
+            try:
+                queue.put_nowait(payload)
+            except asyncio.QueueFull:
+                # Drop oldest event to make room
+                with contextlib.suppress(asyncio.QueueEmpty):
+                    queue.get_nowait()
+                with contextlib.suppress(asyncio.QueueFull):
+                    queue.put_nowait(payload)
+
+        unsubscribe = event_bus.subscribe("*", on_event)
+
+        try:
+            while True:
+                try:
+                    payload = await asyncio.wait_for(queue.get(), timeout=30.0)
+                    yield f"event: {payload['event']}\ndata: {json.dumps(payload)}\n\n"
+                except asyncio.TimeoutError:
+                    yield ":ping\n\n"
+        except asyncio.CancelledError:
+            # Client disconnected
+            raise
+        finally:
+            unsubscribe()
+            _connection_counts[user_id] = max(0, _connection_counts.get(user_id, 1) - 1)
+            if _connection_counts[user_id] == 0:
+                _connection_counts.pop(user_id, None)
+
+    return StreamingResponse(
+        event_generator(),
+        media_type="text/event-stream",
+        headers={
+            "Cache-Control": "no-cache",
+            "Connection": "keep-alive",
+            "X-Accel-Buffering": "no",
+        },
+    )

apps/api/src/api/system/health.py

@@ -5,10 +5,16 @@ from datetime import datetime, timezone
 from typing import Any
 
 from fastapi import APIRouter
-from pydantic import BaseModel, Field
 from sqlalchemy import text
 
 from src.database import SessionLocal
+from src.schemas.system import (
+    DatabaseHealth,
+    DatabaseHealthResponse,
+    DiskHealth,
+    HealthChecks,
+    HealthResponse,
+)
 
 router = APIRouter()
 
@@ -16,45 +22,6 @@ router = APIRouter()
 _start_time = time.time()
 
 
-class DatabaseHealth(BaseModel):
-    """Database health check result."""
-
-    status: str = Field(description="Database health status", examples=["healthy"])
-    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
-
-
-class DiskHealth(BaseModel):
-    """Disk space health check result."""
-
-    status: str = Field(description="Disk health status", examples=["healthy"])
-    free_gb: float = Field(description="Free disk space in GB", examples=[45.2])
-    total_gb: float = Field(description="Total disk space in GB", examples=[100.0])
-
-
-class HealthChecks(BaseModel):
-    """Individual health checks."""
-
-    database: DatabaseHealth | None = None
-    disk: DiskHealth | None = None
-
-
-class HealthResponse(BaseModel):
-    """Overall health check response."""
-
-    status: str = Field(description="Overall health status", examples=["healthy"])
-    timestamp: str = Field(description="ISO 8601 timestamp", examples=["2026-05-19T12:00:00Z"])
-    version: str = Field(description="API version", examples=["0.1.0"])
-    checks: HealthChecks = Field(description="Individual health checks")
-    uptime_seconds: float = Field(description="Server uptime in seconds", examples=[3600.0])
-
-
-class DatabaseHealthResponse(BaseModel):
-    """Database-specific health check response."""
-
-    status: str = Field(description="Database health status", examples=["healthy"])
-    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
-
-
 @router.get(
     "/health",
     response_model=HealthResponse,

apps/api/src/api/system/instance_proxy.py

@@ -8,8 +8,8 @@ from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import ToolInstance
+from src.models import ToolType
 
 logger = logging.getLogger(__name__)
 

apps/api/src/api/system/notifications.py

@@ -0,0 +1,161 @@
+"""Notification API endpoints."""
+
+import uuid
+from datetime import datetime
+
+from fastapi import APIRouter, Depends, HTTPException, Query, status
+from pydantic import BaseModel, ConfigDict, Field
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_current_user, get_db_session
+from src.models.user import User
+from src.models import UserConfig
+from src.services.shared.notification_service import notification_service
+
+router = APIRouter(prefix="/notifications", tags=["notifications"])
+
+
+class NotificationItem(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+    id: uuid.UUID
+    user_id: uuid.UUID
+    category: str
+    severity: str
+    title: str
+    message: str | None
+    source_type: str | None
+    source_id: uuid.UUID | None
+    notification_metadata: dict = Field(serialization_alias="metadata")
+    read_at: datetime | None
+    dismissed_at: datetime | None
+    created_at: datetime
+
+
+class NotificationListResponse(BaseModel):
+    items: list[NotificationItem]
+    total: int
+    limit: int
+    offset: int
+
+
+class UnreadCountResponse(BaseModel):
+    count: int
+
+
+class MarkAllReadResponse(BaseModel):
+    marked_count: int
+
+
+class ClearAllResponse(BaseModel):
+    cleared_count: int
+
+
+async def _get_mute_categories(
+    session: AsyncSession,
+    user_id: uuid.UUID,
+) -> list[str]:
+    """Read notification mute categories from user config."""
+    from sqlalchemy import select
+
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
+    )
+    config = result.scalar_one_or_none()
+    if config is None:
+        return []
+    mute_categories = config.config.get("notification_mute_categories", [])
+    if isinstance(mute_categories, list):
+        return mute_categories
+    return []
+
+
+@router.get("", response_model=NotificationListResponse)
+async def list_notifications(
+    limit: int = Query(20, ge=1, le=100),
+    offset: int = Query(0, ge=0),
+    unread_only: bool = Query(False),
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> NotificationListResponse:
+    """List notifications for the authenticated user."""
+    mute_categories = await _get_mute_categories(session, user.id)
+    items, total = await notification_service.list_notifications(
+        session,
+        user.id,
+        limit=limit,
+        offset=offset,
+        unread_only=unread_only,
+        mute_categories=mute_categories,
+    )
+    return NotificationListResponse(
+        items=[NotificationItem.model_validate(item) for item in items],
+        total=total,
+        limit=limit,
+        offset=offset,
+    )
+
+
+@router.get("/unread", response_model=UnreadCountResponse)
+async def get_unread_count(
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> UnreadCountResponse:
+    """Get unread notification count for the authenticated user."""
+    count = await notification_service.get_unread_count(session, user.id)
+    return UnreadCountResponse(count=count)
+
+
+@router.patch("/{notification_id}/read", response_model=NotificationItem)
+async def mark_notification_read(
+    notification_id: uuid.UUID,
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> NotificationItem:
+    """Mark a single notification as read."""
+    try:
+        notification = await notification_service.mark_read(
+            session, notification_id, user.id
+        )
+    except ValueError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail="Notification not found",
+        ) from exc
+    return NotificationItem.model_validate(notification)
+
+
+@router.post("/mark-all-read", response_model=MarkAllReadResponse)
+async def mark_all_read(
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> MarkAllReadResponse:
+    """Mark all unread notifications as read."""
+    marked = await notification_service.mark_all_read(session, user.id)
+    return MarkAllReadResponse(marked_count=marked)
+
+
+@router.delete("", status_code=status.HTTP_200_OK)
+async def clear_all_notifications(
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> ClearAllResponse:
+    """Dismiss all notifications for the authenticated user."""
+    cleared = await notification_service.dismiss_all(session, user.id)
+    return ClearAllResponse(cleared_count=cleared)
+
+
+@router.delete("/{notification_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def dismiss_notification(
+    notification_id: uuid.UUID,
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Soft-delete (dismiss) a single notification."""
+    try:
+        await notification_service.dismiss(session, notification_id, user.id)
+    except ValueError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail="Notification not found",
+        ) from exc

apps/api/src/api/system/terminal.py

@@ -0,0 +1,872 @@
+"""WebSocket terminal endpoint for tool instances."""
+
+import asyncio
+import json
+import logging
+from asyncio import QueueFull
+from json import JSONDecodeError
+import uuid
+from contextlib import suppress
+
+from fastapi import APIRouter, Depends, HTTPException, WebSocket, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+from starlette.websockets import WebSocketDisconnect
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models import (
+    TerminalSessionModel,
+    ToolDefinitionManifest,
+    ToolInstance,
+    ToolType,
+)
+from src.services.build.manifest_compiler import (
+    deep_merge,
+    get_manifest_container_user,
+    resolve_base,
+)
+from src.services.terminal.terminal_manager import (
+    MaxSessionsExceededError,
+    terminal_manager,
+)
+
+router = APIRouter()
+logger = logging.getLogger(__name__)
+
+MAX_PENDING_INPUT_MESSAGES = 64
+MAX_TERMINAL_INPUT_BYTES = 1024 * 1024
+
+
+class SessionRef:
+    """Mutable reference to a terminal session, allowing updates during reset."""
+
+    def __init__(self, session, slot_session_id: str | None = None):
+        self.session = session
+        self.slot_session_id = slot_session_id or session.session_id
+
+
+@router.websocket(
+    "/ws/tool-instances/{instance_id}/terminal",
+)
+async def terminal_websocket_default(
+    websocket: WebSocket,
+    instance_id: str,
+    db_session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """WebSocket endpoint for terminal access (default session alias).
+
+    Backward-compatible route that maps to the default session.
+    """
+    await _handle_terminal_websocket(websocket, instance_id, None, db_session)
+
+
+@router.websocket(
+    "/ws/tool-instances/{instance_id}/terminal/{session_id}",
+)
+async def terminal_websocket_specific(
+    websocket: WebSocket,
+    instance_id: str,
+    session_id: str,
+    db_session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """WebSocket endpoint for a specific terminal session."""
+    await _handle_terminal_websocket(websocket, instance_id, session_id, db_session)
+
+
+async def _resolve_container_user(
+    db_session: AsyncSession,
+    instance: ToolInstance,
+) -> str | None:
+    """Resolve the container user for docker exec from the tool manifest.
+
+    For manifest-based tools, the user declared in the manifest (or its base
+    definition) is returned so terminal sessions run with the same privileges
+    as the main container process. Legacy tools return None, preserving the
+    previous behavior.
+    """
+    tool_type = await db_session.get(ToolType, instance.tool_type_id)
+    if not tool_type or tool_type.definition_type != "manifest":
+        return None
+
+    if not tool_type.manifest_id:
+        return None
+
+    manifest_def = await db_session.get(ToolDefinitionManifest, tool_type.manifest_id)
+    if not manifest_def:
+        return None
+
+    manifest = dict(manifest_def.manifest)
+    if manifest_def.base_definition_id:
+        base_def = await db_session.get(
+            ToolDefinitionManifest, manifest_def.base_definition_id
+        )
+        if base_def:
+            manifest = resolve_base(deep_merge(dict(base_def.manifest), manifest))
+
+    return get_manifest_container_user(manifest)
+
+
+async def _handle_terminal_websocket(
+    websocket: WebSocket,
+    instance_id: str,
+    target_session_id: str | None,
+    db_session: AsyncSession,
+) -> None:
+    """Shared WebSocket handler for terminal sessions.
+
+    Args:
+        websocket: The WebSocket connection.
+        instance_id: UUID string of the tool instance.
+        target_session_id: Specific session ID (slot key). None means default session.
+        db_session: Database session.
+    """
+    logger.debug(
+        "Terminal WebSocket connection attempt for instance %s (session=%s)",
+        instance_id,
+        target_session_id or "default",
+    )
+    await websocket.accept()
+    logger.debug("Terminal WebSocket accepted for instance %s", instance_id)
+
+    try:
+        # Parse instance_id
+        instance_uuid = uuid.UUID(instance_id)
+    except ValueError:
+        logger.error("Invalid instance ID: %s", instance_id)
+        await websocket.close(code=4001, reason="Invalid instance ID")
+        return
+
+    # Authenticate user from session cookie
+    user_id = await _get_user_from_websocket(websocket, db_session)
+    if user_id is None:
+        logger.warning(
+            "Unauthorized terminal access attempt for instance %s", instance_id
+        )
+        await websocket.close(code=4003, reason="Unauthorized")
+        return
+
+    # Get instance and verify ownership
+    instance = await db_session.get(ToolInstance, instance_uuid)
+    if instance is None:
+        logger.warning("Instance %s not found", instance_id)
+        await websocket.close(code=4004, reason="Instance not found")
+        return
+
+    if instance.owner_id != user_id:
+        logger.warning(
+            "Forbidden terminal access for instance %s by user %s",
+            instance_id,
+            user_id,
+        )
+        await websocket.close(code=4003, reason="Forbidden")
+        return
+
+    if instance.status != "running" or not instance.container_id:
+        logger.warning(
+            "Instance %s not running (status=%s, container_id=%s)",
+            instance_id,
+            instance.status,
+            instance.container_id,
+        )
+        await websocket.close(code=4004, reason="Instance not running")
+        return
+
+    logger.debug("Terminal auth passed for instance %s, user %s", instance_id, user_id)
+
+    # Verify the container actually exists (may have been removed/recreated)
+    from src.services.docker import get_container_status
+
+    container_status = get_container_status(instance.container_id)
+    if container_status["status"] == "not_found":
+        logger.error(
+            "Container %s for instance %s not found (may have been removed)",
+            instance.container_id,
+            instance_id,
+        )
+        await websocket.close(
+            code=4004, reason="Container not found — restart the tool instance"
+        )
+        return
+
+    # Fetch tool type to get startup_command and container_user
+    tool_type = await db_session.get(ToolType, instance.tool_type_id)
+    startup_command = tool_type.startup_command if tool_type else None
+    if startup_command:
+        logger.debug(
+            "Using startup command for instance %s: %s",
+            instance_id,
+            startup_command,
+        )
+
+    container_user = await _resolve_container_user(db_session, instance)
+    if container_user:
+        logger.debug(
+            "Terminal sessions for instance %s will run as user %s",
+            instance_id,
+            container_user,
+        )
+
+    session = None
+
+    # Get or create terminal session
+    try:
+        if target_session_id is None:
+            # Default session alias
+            session = await terminal_manager.get_or_create_session(
+                instance_uuid,
+                instance.container_id,
+                startup_command=startup_command,
+                container_user=container_user,
+            )
+            slot_session_id = "default"
+        else:
+            # Specific session
+            session = terminal_manager.get_session(
+                instance_id,
+                target_session_id,
+            )
+            if session is None:
+                # Session not in memory — may have been lost on server restart.
+                # Try to restore from the DB row.
+                db_row = await db_session.get(
+                    TerminalSessionModel, uuid.UUID(target_session_id)
+                )
+                if (
+                    db_row is not None
+                    and db_row.instance_id == instance_uuid
+                    and db_row.status != "closed"
+                ):
+                    logger.info(
+                        "Restoring terminal session %s for instance %s from DB",
+                        target_session_id,
+                        instance_id,
+                    )
+                    session = await terminal_manager.create_session(
+                        instance_uuid,
+                        instance.container_id,
+                        startup_command=startup_command,
+                        name=db_row.name,
+                        session_id=target_session_id,
+                        container_user=container_user,
+                    )
+                else:
+                    logger.warning(
+                        "Session %s not found for instance %s",
+                        target_session_id,
+                        instance_id,
+                    )
+                    await websocket.close(code=4004, reason="Session not found")
+                    return
+            # Determine slot key for reset scoping
+            key = terminal_manager._find_key_by_internal_id(
+                instance_id, session.session_id
+            )
+            slot_session_id = key[1] if key else target_session_id
+
+        logger.debug(
+            "Terminal session ready for instance %s (session_id=%s, slot=%s)",
+            instance_id,
+            session.session_id,
+            slot_session_id,
+        )
+
+        # Attach WebSocket to session
+        await terminal_manager.attach_websocket(session, websocket)
+        logger.debug("WebSocket attached to session for instance %s", instance_id)
+
+        # Send connected status
+        await websocket.send_json({"type": "status", "status": "connected"})
+        logger.debug("Sent connected status for instance %s", instance_id)
+
+        # Use mutable session reference so loops can survive reset
+        session_ref = SessionRef(session, slot_session_id)
+
+        # Start write loop and heartbeat (read is now event-driven in TerminalSession)
+        write_task = asyncio.create_task(
+            _write_loop(session_ref, websocket, instance_id)
+        )
+        heartbeat_task = asyncio.create_task(_heartbeat_loop(websocket))
+        logger.debug("Started terminal loops for instance %s", instance_id)
+
+        # Wait for either task to complete (indicating disconnect or error)
+        done, pending = await asyncio.wait(
+            [write_task, heartbeat_task],
+            return_when=asyncio.FIRST_COMPLETED,
+        )
+
+        logger.debug(
+            "Terminal loop completed for instance %s, done=%s",
+            instance_id,
+            len(done),
+        )
+
+        # Cancel remaining tasks
+        for task in pending:
+            task.cancel()
+
+    except WebSocketDisconnect:
+        logger.debug("WebSocket disconnected for instance %s", instance_id)
+    except Exception as exc:
+        logger.error(
+            "Terminal session error for instance %s: %s",
+            instance_id,
+            str(exc),
+            exc_info=True,
+        )
+        with suppress(Exception):
+            await websocket.close(code=4000, reason=f"Error: {exc}")
+    finally:
+        # Detach WebSocket, don't kill session
+        with suppress(Exception):
+            if session is not None:
+                await terminal_manager.detach_websocket(session, websocket)
+                logger.debug(
+                    "WebSocket detached from session for instance %s", instance_id
+                )
+
+
+async def _input_write_loop(input_queue: asyncio.Queue[tuple[object, bytes]]) -> None:
+    """Serialize PTY writes without blocking terminal control messages."""
+    while True:
+        session, data = await input_queue.get()
+        try:
+            await session.write_input(data)  # type: ignore[attr-defined]
+        except Exception:
+            logger.debug("Terminal input write failed", exc_info=True)
+        finally:
+            input_queue.task_done()
+
+
+def _queue_terminal_input(
+    input_queue: asyncio.Queue[tuple[object, bytes]], session: object, data: bytes
+) -> bool:
+    """Queue bounded terminal input without blocking control-message processing."""
+    if len(data) > MAX_TERMINAL_INPUT_BYTES:
+        return False
+    try:
+        input_queue.put_nowait((session, data))
+    except QueueFull:
+        return False
+    return True
+
+
+async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> None:
+    """Receive terminal messages while a dedicated worker serializes PTY input."""
+    input_queue: asyncio.Queue[tuple[object, bytes]] = asyncio.Queue(
+        maxsize=MAX_PENDING_INPUT_MESSAGES
+    )
+    input_writer = asyncio.create_task(_input_write_loop(input_queue))
+
+    try:
+        while True:
+            session = session_ref.session
+            if not session.is_alive() or session._closed:
+                await asyncio.sleep(0.1)
+                continue
+            message = await websocket.receive()
+            if message["type"] == "websocket.receive":
+                if "bytes" in message:
+                    if not _queue_terminal_input(
+                        input_queue, session, message["bytes"]
+                    ):
+                        logger.warning("Terminal input buffer exceeded for %s", instance_id)
+                        await websocket.close(code=1009, reason="Terminal input buffer full")
+                        break
+                elif "text" in message:
+                    text = message["text"]
+                    # A text frame that parses to a JSON object with a
+                    # "type" field is a control message and must NEVER be
+                    # written to the PTY (e.g. the heartbeat {"type":"pong"}
+                    # must be consumed, not typed into the shell/pi). Handle
+                    # known types and ignore unknown ones. Everything else
+                    # (keystrokes, bracketed-paste content, plain text) is
+                    # forwarded as raw terminal input.
+                    ctrl = None
+                    if text.startswith("{"):
+                        try:
+                            parsed = json.loads(text)
+                        except JSONDecodeError:
+                            parsed = None
+                        if isinstance(parsed, dict) and "type" in parsed:
+                            ctrl = parsed
+
+                    if ctrl is None:
+                        if not _queue_terminal_input(
+                            input_queue, session, text.encode("utf-8")
+                        ):
+                            logger.warning(
+                                "Terminal input buffer exceeded for %s", instance_id
+                            )
+                            await websocket.close(
+                                code=1009, reason="Terminal input buffer full"
+                            )
+                            break
+                        continue
+
+                    msg_type = ctrl["type"]
+                    if msg_type == "resize":
+                        cols = ctrl.get("cols", 80)
+                        rows = ctrl.get("rows", 24)
+                        logger.debug(
+                            "Received resize message for instance %s: %sx%s",
+                            instance_id,
+                            cols,
+                            rows,
+                        )
+                        await session.resize(cols, rows)
+                    elif msg_type == "ack":
+                        char_count = ctrl.get("chars", 0)
+                        if char_count > 0:
+                            session.acknowledge_data(char_count)
+                    elif msg_type == "reset":
+                        # Reset terminal session (scoped to current slot)
+                        logger.debug(
+                            "Resetting terminal session for instance %s (slot=%s)",
+                            session.instance_id,
+                            session_ref.slot_session_id,
+                        )
+                        await websocket.send_json(
+                            {"type": "status", "status": "resetting"}
+                        )
+
+                        # Reset the session scoped to its slot
+                        new_session = await terminal_manager.reset_session(
+                            session.instance_id,
+                            session.container_id,
+                            startup_command=session.startup_command,
+                            session_id=session_ref.slot_session_id,
+                            name=session.name,
+                            container_user=session.container_user,
+                        )
+
+                        # Update the mutable session reference
+                        session_ref.session = new_session
+
+                        # Attach to new session
+                        await terminal_manager.attach_websocket(new_session, websocket)
+                        await websocket.send_json(
+                            {"type": "status", "status": "connected"}
+                        )
+
+                        # Continue the loop with the new session
+                        continue
+            elif message["type"] == "websocket.disconnect":
+                break
+    except WebSocketDisconnect:
+        pass
+    except (RuntimeError, TypeError, ValueError) as exc:
+        logger.debug("Terminal WebSocket receive loop ended: %s", exc)
+    finally:
+        input_writer.cancel()
+        with suppress(asyncio.CancelledError):
+            await input_writer
+
+
+async def _heartbeat_loop(websocket: WebSocket) -> None:
+    """Send periodic ping messages to detect disconnections."""
+    try:
+        while True:
+            await asyncio.sleep(30)  # Ping every 30 seconds
+            try:
+                await websocket.send_json({"type": "ping"})
+            except Exception:
+                # WebSocket is closed or broken
+                break
+    except Exception:
+        pass
+
+
+async def _get_terminal_instance(
+    instance_id: uuid.UUID,
+    user_id: uuid.UUID,
+    db_session: AsyncSession,
+) -> ToolInstance:
+    """Fetch instance and validate auth, ownership, and running status.
+
+    Args:
+        instance_id: UUID of the tool instance.
+        user_id: ID of the authenticated user.
+        db_session: Database session.
+
+    Returns:
+        The validated ToolInstance.
+
+    Raises:
+        HTTPException: If instance not found, not owned, or not running.
+    """
+    instance = await db_session.get(ToolInstance, instance_id)
+    if instance is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Instance not found"
+        )
+
+    if instance.owner_id != user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN,
+            detail="Not authorized to access this instance",
+        )
+
+    if instance.status != "running" or not instance.container_id:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST, detail="Instance is not running"
+        )
+
+    return instance
+
+
+@router.get(
+    "/instances/{instance_id}/terminal/sessions",
+    summary="List terminal sessions",
+    description="List terminal sessions for a tool instance with live WebSocket state.",
+)
+async def list_terminal_sessions(
+    instance_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    db_session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """List terminal sessions for an instance.
+
+    Args:
+        instance_id: UUID of the tool instance.
+        user_id: ID of the authenticated user.
+        db_session: Database session.
+
+    Returns:
+        Dictionary with sessions list.
+    """
+    await _get_terminal_instance(instance_id, user_id, db_session)
+
+    # Query active DB rows for this instance
+    result = await db_session.execute(
+        select(TerminalSessionModel)
+        .where(TerminalSessionModel.instance_id == instance_id)
+        .where(TerminalSessionModel.status != "closed")
+        .order_by(TerminalSessionModel.created_at.asc())
+    )
+    db_rows = result.scalars().all()
+
+    # Build response with live has_websockets flag.
+    # Include DB rows even without in-memory counterparts (e.g. after
+    # server restart) so the frontend can display tabs and reconnect.
+    sessions = []
+    for row in db_rows:
+        live_session = terminal_manager.get_session(str(instance_id), str(row.id))
+        sessions.append(
+            {
+                "id": str(row.id),
+                "name": row.name,
+                "status": row.status,
+                "has_websockets": live_session.has_websockets()
+                if live_session
+                else False,
+                "created_at": row.created_at.isoformat() if row.created_at else None,
+                "last_activity_at": row.last_activity_at.isoformat()
+                if row.last_activity_at
+                else None,
+            }
+        )
+
+    return {"sessions": sessions}
+
+
+@router.post(
+    "/instances/{instance_id}/terminal/sessions",
+    summary="Create terminal session",
+    description="Create a new terminal session for a running tool instance.",
+    status_code=status.HTTP_201_CREATED,
+)
+async def create_terminal_session(
+    instance_id: uuid.UUID,
+    data: dict,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    db_session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Create a new terminal session.
+
+    Args:
+        instance_id: UUID of the tool instance.
+        data: Request body with optional name.
+        user_id: ID of the authenticated user.
+        db_session: Database session.
+
+    Returns:
+        Dictionary with new session details.
+
+    Raises:
+        HTTPException: 409 if max sessions reached.
+    """
+    instance = await _get_terminal_instance(instance_id, user_id, db_session)
+    assert instance.container_id is not None
+
+    # Fetch tool type to get startup_command
+    tool_type = await db_session.get(ToolType, instance.tool_type_id)
+    startup_command = tool_type.startup_command if tool_type else None
+
+    name = data.get("name")
+    container_user = await _resolve_container_user(db_session, instance)
+
+    try:
+        session = await terminal_manager.create_session(
+            instance_id,
+            instance.container_id,
+            startup_command=startup_command,
+            name=name,
+            container_user=container_user,
+        )
+    except MaxSessionsExceededError:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail="Maximum of 5 terminal sessions reached for this instance",
+        ) from None
+
+    return {
+        "id": session.session_id,
+        "name": session.name,
+        "status": session.status,
+        "created_at": session.last_activity,
+    }
+
+
+@router.delete(
+    "/instances/{instance_id}/terminal/sessions/{session_id}",
+    summary="Close terminal session",
+    description="Close a specific terminal session.",
+)
+async def close_terminal_session(
+    instance_id: uuid.UUID,
+    session_id: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    db_session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Close a terminal session.
+
+    Args:
+        instance_id: UUID of the tool instance.
+        session_id: ID of the session to close.
+        user_id: ID of the authenticated user.
+        db_session: Database session.
+
+    Returns:
+        Dictionary with closure status.
+    """
+    await _get_terminal_instance(instance_id, user_id, db_session)
+
+    # Find the session by internal ID to determine its slot key
+    key = terminal_manager._find_key_by_internal_id(str(instance_id), session_id)
+    if (
+        key is None
+        and terminal_manager.get_session(str(instance_id), session_id) is not None
+    ):
+        key = (str(instance_id), session_id)
+
+    if key is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Session not found"
+        )
+
+    await terminal_manager.close_session(key[0], key[1])
+
+    return {"status": "closed", "session_id": session_id}
+
+
+@router.post(
+    "/instances/{instance_id}/terminal/sessions/{session_id}/reset",
+    summary="Reset terminal session",
+    description="Reset a specific terminal session, killing the current shell and starting fresh.",
+)
+async def reset_specific_terminal_session(
+    instance_id: uuid.UUID,
+    session_id: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    db_session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Reset a specific terminal session.
+
+    Args:
+        instance_id: UUID of the tool instance.
+        session_id: ID of the session to reset.
+        user_id: ID of the authenticated user.
+        db_session: Database session.
+
+    Returns:
+        Dictionary with reset session details.
+    """
+    instance = await _get_terminal_instance(instance_id, user_id, db_session)
+    assert instance.container_id is not None
+
+    # Determine slot key for reset
+    key = terminal_manager._find_key_by_internal_id(str(instance_id), session_id)
+    if (
+        key is None
+        and terminal_manager.get_session(str(instance_id), session_id) is not None
+    ):
+        key = (str(instance_id), session_id)
+
+    if key is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Session not found"
+        )
+
+    # Fetch tool type to get startup_command
+    tool_type = await db_session.get(ToolType, instance.tool_type_id)
+    startup_command = tool_type.startup_command if tool_type else None
+
+    # Preserve name if possible
+    live_session = terminal_manager.get_session(str(instance_id), session_id)
+    name = live_session.name if live_session else None
+    container_user = await _resolve_container_user(db_session, instance)
+
+    new_session = await terminal_manager.reset_session(
+        instance_id,
+        instance.container_id,
+        startup_command=startup_command,
+        session_id=key[1],
+        name=name,
+        container_user=container_user,
+    )
+
+    return {
+        "id": new_session.session_id,
+        "name": new_session.name,
+        "status": new_session.status,
+    }
+
+
+@router.post(
+    "/instances/{instance_id}/terminal/sessions/{session_id}/rename",
+    summary="Rename terminal session",
+    description="Rename a specific terminal session.",
+)
+async def rename_terminal_session(
+    instance_id: uuid.UUID,
+    session_id: str,
+    data: dict,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    db_session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Rename a terminal session.
+
+    Args:
+        instance_id: UUID of the tool instance.
+        session_id: ID of the session to rename.
+        data: Request body with new name.
+        user_id: ID of the authenticated user.
+        db_session: Database session.
+
+    Returns:
+        Dictionary with updated session details.
+    """
+    await _get_terminal_instance(instance_id, user_id, db_session)
+
+    new_name = data.get("name")
+    if not new_name or not isinstance(new_name, str):
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST, detail="Name is required"
+        )
+
+    # Update in-memory session name if live
+    live_session = terminal_manager.get_session(str(instance_id), session_id)
+    if live_session:
+        live_session.name = new_name
+
+    # Update DB row
+    db_row = await db_session.get(TerminalSessionModel, uuid.UUID(session_id))
+    if db_row is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Session not found"
+        )
+
+    db_row.name = new_name
+    await db_session.commit()
+
+    return {"id": str(db_row.id), "name": new_name}
+
+
+@router.post(
+    "/instances/{instance_id}/terminal/reset",
+    summary="Reset terminal session (legacy alias)",
+    description="Reset the default terminal session for a tool instance. Preserved for backward compatibility.",
+)
+async def reset_terminal_session(
+    instance_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    db_session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Reset the default terminal session for an instance (legacy alias).
+
+    Args:
+        instance_id: UUID of the tool instance.
+        user_id: ID of the authenticated user.
+        db_session: Database session.
+
+    Returns:
+        Dictionary with status message.
+    """
+    instance = await _get_terminal_instance(instance_id, user_id, db_session)
+    assert instance.container_id is not None
+
+    # Fetch tool type to get startup_command
+    tool_type = await db_session.get(ToolType, instance.tool_type_id)
+    startup_command = tool_type.startup_command if tool_type else None
+    container_user = await _resolve_container_user(db_session, instance)
+
+    try:
+        # Reset the default session
+        new_session = await terminal_manager.reset_session(
+            instance_id,
+            instance.container_id,
+            startup_command=startup_command,
+            container_user=container_user,
+        )
+
+        logger.info(
+            "Terminal session reset for instance %s (new session_id=%s)",
+            instance_id,
+            new_session.session_id,
+        )
+
+        return {
+            "status": "success",
+            "message": "Terminal session reset successfully",
+            "instance_id": str(instance_id),
+            "session_id": new_session.session_id,
+        }
+    except Exception as exc:
+        logger.error(
+            "Failed to reset terminal session for instance %s: %s",
+            instance_id,
+            str(exc),
+            exc_info=True,
+        )
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+            detail=f"Failed to reset terminal session: {exc}",
+        ) from exc
+
+
+async def _get_user_from_websocket(
+    websocket: WebSocket,
+    db_session: AsyncSession,
+) -> uuid.UUID | None:
+    """Extract and validate user ID from session cookie in WebSocket.
+
+    Args:
+        websocket: The WebSocket connection.
+        db_session: Database session.
+
+    Returns:
+        The user's UUID if authenticated, None otherwise.
+    """
+    from src.auth.session import decode_session_cookie
+    from src.config import Settings
+
+    session_cookie = websocket.cookies.get("session")
+    if not session_cookie:
+        return None
+
+    settings = Settings()
+    try:
+        payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
+        return uuid.UUID(str(payload["user_id"]))
+    except (ValueError, KeyError):
+        return None

apps/api/src/api/terminal.py

@@ -1,324 +0,0 @@
-"""WebSocket terminal endpoint for tool instances."""
-
-import asyncio
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, WebSocket, status
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_db_session
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.services.terminal_manager import terminal_manager
-
-router = APIRouter()
-logger = logging.getLogger(__name__)
-
-
-class SessionRef:
-    """Mutable reference to a terminal session, allowing updates during reset."""
-
-    def __init__(self, session):
-        self.session = session
-
-
-@router.websocket(
-    "/ws/tool-instances/{instance_id}/terminal",
-)
-async def terminal_websocket(
-    websocket: WebSocket,
-    instance_id: str,
-    db_session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """WebSocket endpoint for terminal access to a tool instance.
-
-    Provides an interactive terminal session inside a running tool instance container.
-    Sessions persist across WebSocket disconnections.
-
-    Args:
-        websocket: The WebSocket connection.
-        instance_id: UUID string of the tool instance.
-        db_session: Database session.
-
-    Returns:
-        None. Communicates via WebSocket messages.
-    """
-    logger.debug("Terminal WebSocket connection attempt for instance %s", instance_id)
-    await websocket.accept()
-    logger.debug("Terminal WebSocket accepted for instance %s", instance_id)
-
-    try:
-        # Parse instance_id
-        instance_uuid = uuid.UUID(instance_id)
-    except ValueError:
-        logger.error("Invalid instance ID: %s", instance_id)
-        await websocket.close(code=4001, reason="Invalid instance ID")
-        return
-
-    # Authenticate user from session cookie
-    user_id = await _get_user_from_websocket(websocket, db_session)
-    if user_id is None:
-        logger.warning("Unauthorized terminal access attempt for instance %s", instance_id)
-        await websocket.close(code=4003, reason="Unauthorized")
-        return
-
-    # Get instance and verify ownership
-    instance = await db_session.get(ToolInstance, instance_uuid)
-    if instance is None:
-        logger.warning("Instance %s not found", instance_id)
-        await websocket.close(code=4004, reason="Instance not found")
-        return
-
-    if instance.owner_id != user_id:
-        logger.warning("Forbidden terminal access for instance %s by user %s", instance_id, user_id)
-        await websocket.close(code=4003, reason="Forbidden")
-        return
-
-    if instance.status != "running" or not instance.container_id:
-        logger.warning("Instance %s not running (status=%s, container_id=%s)", instance_id, instance.status, instance.container_id)
-        await websocket.close(code=4004, reason="Instance not running")
-        return
-
-    logger.debug("Terminal auth passed for instance %s, user %s", instance_id, user_id)
-
-    # Fetch tool type to get startup_command
-    tool_type = await db_session.get(ToolType, instance.tool_type_id)
-    startup_command = tool_type.startup_command if tool_type else None
-    if startup_command:
-        logger.debug("Using startup command for instance %s: %s", instance_id, startup_command)
-
-    # Get or create terminal session
-    try:
-        session = await terminal_manager.get_or_create_session(
-            instance_uuid,
-            instance.container_id,
-            startup_command=startup_command,
-        )
-        logger.debug("Terminal session ready for instance %s (session_id=%s)", instance_id, session.session_id)
-
-        # Attach WebSocket to session
-        await terminal_manager.attach_websocket(session, websocket)
-        logger.debug("WebSocket attached to session for instance %s", instance_id)
-
-        # Send connected status
-        await websocket.send_json({"type": "status", "status": "connected"})
-        logger.debug("Sent connected status for instance %s", instance_id)
-
-        # Use mutable session reference so loops can survive reset
-        session_ref = SessionRef(session)
-
-        # Start I/O loops and heartbeat
-        read_task = asyncio.create_task(_read_loop(session_ref, websocket))
-        write_task = asyncio.create_task(_write_loop(session_ref, websocket, instance_id))
-        heartbeat_task = asyncio.create_task(_heartbeat_loop(websocket))
-        logger.debug("Started terminal loops for instance %s", instance_id)
-
-        # Wait for either task to complete (indicating disconnect or error)
-        done, pending = await asyncio.wait(
-            [read_task, write_task, heartbeat_task],
-            return_when=asyncio.FIRST_COMPLETED,
-        )
-        
-        logger.debug("Terminal loop completed for instance %s, done=%s", instance_id, len(done))
-        
-        # Cancel remaining tasks
-        for task in pending:
-            task.cancel()
-
-    except Exception as exc:
-        logger.error("Terminal session error for instance %s: %s", instance_id, str(exc), exc_info=True)
-        await websocket.close(code=4000, reason=f"Error: {exc}")
-    finally:
-        # Detach WebSocket, don't kill session
-        try:
-            if 'session' in locals():
-                await terminal_manager.detach_websocket(session, websocket)
-                logger.debug("WebSocket detached from session for instance %s", instance_id)
-        except Exception:
-            pass
-
-
-async def _read_loop(session_ref: SessionRef, websocket) -> None:
-    """Read output from the container and send to WebSocket."""
-    try:
-        while True:
-            session = session_ref.session
-            if not session.is_alive() or session._closed:
-                await asyncio.sleep(0.1)
-                continue
-            data = await session.read_output()
-            if data:
-                try:
-                    await websocket.send_bytes(data)
-                except Exception:
-                    break
-            else:
-                await asyncio.sleep(0.01)
-    except Exception:
-        pass
-
-
-async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> None:
-    """Read input from WebSocket and send to container."""
-    try:
-        while True:
-            session = session_ref.session
-            if not session.is_alive() or session._closed:
-                await asyncio.sleep(0.1)
-                continue
-            message = await websocket.receive()
-            if message["type"] == "websocket.receive":
-                if "bytes" in message:
-                    await session.write_input(message["bytes"])
-                elif "text" in message:
-                    text = message["text"]
-                    if text.startswith("{"):
-                        # Control message (JSON)
-                        import json
-                        try:
-                            ctrl = json.loads(text)
-                            msg_type = ctrl.get("type")
-                            
-                            if msg_type == "resize":
-                                cols = ctrl.get("cols", 80)
-                                rows = ctrl.get("rows", 24)
-                                logger.debug(f"Received resize message for instance {instance_id}: {cols}x{rows}")
-                                await session.resize(cols, rows)
-                            elif msg_type == "reset":
-                                # Reset terminal session
-                                logger.debug("Resetting terminal session for instance %s", session.instance_id)
-                                await websocket.send_json({"type": "status", "status": "resetting"})
-                                
-                                # Reset the session
-                                new_session = await terminal_manager.reset_session(
-                                    session.instance_id,
-                                    session.container_id,
-                                    startup_command=session.startup_command,
-                                )
-                                
-                                # Update the mutable session reference so read_loop uses the new session
-                                session_ref.session = new_session
-                                
-                                # Attach to new session
-                                await terminal_manager.attach_websocket(new_session, websocket)
-                                await websocket.send_json({"type": "status", "status": "connected"})
-                                
-                                # Continue the loop with the new session
-                                continue
-                                
-                        except json.JSONDecodeError:
-                            # Not a valid JSON control message, treat as regular input
-                            await session.write_input(text.encode("utf-8"))
-                    else:
-                        await session.write_input(text.encode("utf-8"))
-            elif message["type"] == "websocket.disconnect":
-                break
-    except Exception:
-        pass
-
-
-async def _heartbeat_loop(websocket: WebSocket) -> None:
-    """Send periodic ping messages to detect disconnections."""
-    try:
-        while True:
-            await asyncio.sleep(30)  # Ping every 30 seconds
-            try:
-                await websocket.send_json({"type": "ping"})
-            except Exception:
-                # WebSocket is closed or broken
-                break
-    except Exception:
-        pass
-
-
-@router.post(
-    "/projects/{project_id}/repositories/{repo_id}/instances/{instance_id}/terminal/reset",
-    summary="Reset terminal session",
-    description="Reset the terminal session for a tool instance, killing the current shell and starting fresh.",
-)
-async def reset_terminal_session(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    db_session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Reset the terminal session for an instance.
-
-    Args:
-        project_id: UUID of the project.
-        repo_id: UUID of the repository.
-        instance_id: UUID of the tool instance.
-        db_session: Database session.
-
-    Returns:
-        Dictionary with status message.
-    """
-    # Get instance and verify it exists and is running
-    instance = await db_session.get(ToolInstance, instance_id)
-    if instance is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail="Instance not found"
-        )
-
-    if instance.status != "running" or not instance.container_id:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="Instance is not running"
-        )
-
-    # Fetch tool type to get startup_command
-    tool_type = await db_session.get(ToolType, instance.tool_type_id)
-    startup_command = tool_type.startup_command if tool_type else None
-
-    try:
-        # Reset the session
-        new_session = await terminal_manager.reset_session(
-            instance_id,
-            instance.container_id,
-            startup_command=startup_command,
-        )
-        
-        logger.info("Terminal session reset for instance %s (new session_id=%s)", instance_id, new_session.session_id)
-        
-        return {
-            "status": "success",
-            "message": "Terminal session reset successfully",
-            "instance_id": str(instance_id),
-            "session_id": new_session.session_id,
-        }
-    except Exception as exc:
-        logger.error("Failed to reset terminal session for instance %s: %s", instance_id, str(exc), exc_info=True)
-        raise HTTPException(
-            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
-            detail=f"Failed to reset terminal session: {exc}"
-        )
-
-
-async def _get_user_from_websocket(
-    websocket: WebSocket,
-    db_session: AsyncSession,
-) -> uuid.UUID | None:
-    """Extract and validate user ID from session cookie in WebSocket.
-
-    Args:
-        websocket: The WebSocket connection.
-        db_session: Database session.
-
-    Returns:
-        The user's UUID if authenticated, None otherwise.
-    """
-    from src.auth.session import decode_session_cookie
-    from src.config import Settings
-
-    session_cookie = websocket.cookies.get("session")
-    if not session_cookie:
-        return None
-
-    settings = Settings()
-    try:
-        payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
-        return uuid.UUID(str(payload["user_id"]))
-    except (ValueError, KeyError):
-        return None

apps/api/src/api/tool/.pi-map.index.md

@@ -0,0 +1,26 @@
+# apps/api/src/api/tool (index)
+dir: apps/api/src/api/tool
+
+## role
+Provides FastAPI REST API endpoints for managing containerized tools throughout their lifecycle, including type definitions, instance management, session tracking, and Docker operations.
+## parent
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- sessions.py
+- tool_definitions.py
+- tool_instances.py
+- tool_lifecycle.py
+- tool_types.py
+- tool_types_validation.py
+## links
+index: apps/api/src/api/tool/.pi-map.index.md
+map: apps/api/src/api/tool/.pi-map.md
+## workflows
+- change tool behavior
+  read: __init__.py, sessions.py, tool_definitions.py
+## dirty
+-

apps/api/src/api/tool/.pi-map.md

@@ -0,0 +1,33 @@
+# apps/api/src/api/tool
+dir: apps/api/src/api/tool
+
+index: apps/api/src/api/tool/.pi-map.index.md
+
+## role
+Provides FastAPI REST API endpoints for managing containerized tools throughout their lifecycle, including type definitions, instance management, session tracking, and Docker operations.
+## files
+- __init__.py | Aggregates and exports router modules for the Tool API package. | dep: src.api.tool.sessions, src.api.tool.tool_definitions, src.api.tool.tool_instances, src.api.tool.tool_lifecycle, src.api.tool.tool_types
+- sessions.py | Provides a FastAPI endpoint to retrieve all active tool sessions (running instances) for the currently authenticated user with related metadata. | exp: func:get_user_sessions(user_id, session) → dict, call:_get_user, call:session.execute, call:select(ToolInstance) .where(ToolInstance.owner_id == user_id) .where( ToolInstance.status.in_( ["running", "building", "pending", "stopped", "error"] ) ) .order_by, call:ToolInstance.status.in_, call:ToolInstance.created_at.desc, call:result.scalars().all, call:session.get, call:sessions.append, call:str, call:instance.created_at.isoformat | dep: uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models
+- tool_definitions.py | Provides FastAPI CRUD endpoints for managing tool definition manifests with compilation to Dockerfile and Docker Compose previews. | exp: class:CreateToolDefinitionRequest, class:UpdateToolDefinitionRequest, func:create_tool_definition(data: CreateToolDefinitionRequest, user_id, session) → dict, call:uuid.UUID, call:session.get, call:session.execute, call:select(ToolDefinitionManifest).where, call:existing.scalar_one_or_none, call:ToolDefinitionManifest, call:session.add, call:session.commit, call:session.refresh, call:logger.info, call:str, call:definition.created_at.isoformat, raise:HTTPException, func:list_tool_definitions(user_id, session, include_bases) → dict, call:select, call:query.where, call:ToolDefinitionManifest.is_base.is_, call:session.execute, call:query.order_by, call:ToolDefinitionManifest.created_at.desc, call:result.scalars().all, call:str, call:d.created_at.isoformat, func:get_tool_definition(definition_id: uuid.UUID, user_id, session) → dict, call:session.get, call:str, call:definition.created_at.isoformat, call:definition.updated_at.isoformat, raise:HTTPException, func:update_tool_definition(definition_id: uuid.UUID, data: UpdateToolDefinitionRequest, user_id, session) → dict, call:session.get, call:session.commit, call:session.refresh, call:logger.info, call:str, call:definition.updated_at.isoformat, raise:HTTPException, func:delete_tool_definition(definition_id: uuid.UUID, user_id, session) → dict, call:session.get, call:session.execute, call:select(ToolType).where, call:result.scalars().all, call:", ".join, call:session.delete, call:session.commit, call:logger.info, call:str, raise:HTTPException, func:compile_tool_definition(definition_id: uuid.UUID, user_id, session) → dict, call:session.get, call:dict, call:resolve_base, call:deep_merge, call:compile_dockerfile, call:compile_entrypoint, call:compute_image_tag, call:compile_compose, call:session.commit, call:str, raise:HTTPException | dep: logging, uuid, fastapi, pydantic, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.services.build.manifest_compiler
+- tool_instances.py | FastAPI router providing REST endpoints for managing tool instances (CRUD, logs, health checks, tunnel management, proxying, and event history) within project repositories. | exp: func:create_instance(project_id: uuid.UUID, repo_id: uuid.UUID, data: CreateInstanceRequest, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:create_tool_instance, call:str, call:instance.created_at.isoformat, raise:HTTPException, func:list_instances(project_id: uuid.UUID, repo_id: uuid.UUID, user_id, session) → list[dict], call:_get_user, call:_get_owned_project, call:session.execute, call:select(ToolInstance) .where(ToolInstance.repository_id == repo_id) .where(ToolInstance.owner_id == user_id) .order_by, call:ToolInstance.created_at.desc, call:result.scalars().all, call:str, call:i.created_at.isoformat, func:get_instance(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:session.get, call:get_container_status, call:str, call:instance.created_at.isoformat, call:instance.last_started_at.isoformat, raise:HTTPException, func:rename_instance(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, data: dict, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:data.get("display_name", "").strip, call:rename_tool_instance, call:str, raise:HTTPException, func:get_instance_logs(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, tail, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:session.get, call:get_container_logs, raise:HTTPException, func:recreate_tunnel_endpoint(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:recreate_instance_tunnel, raise:HTTPException, func:check_instance_tunnel_health(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:session.get, call:get_container_status, call:instance.probe_result.get, call:"\n".join, call:check_tunnel_health, call:tunnel_health.get, raise:HTTPException, func:get_instance_events(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, limit, user_id, session) → list[dict], call:_get_user, call:_get_owned_project, call:session.get, call:session.execute, call:select(InstanceEvent) .where(InstanceEvent.instance_id == instance_id) .order_by(InstanceEvent.created_at.desc()) .limit, call:InstanceEvent.created_at.desc, call:result.scalars().all, call:str, call:row.created_at.isoformat, raise:HTTPException, func:proxy_to_instance(request: Request, project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, path, user_id, session) → Response, call:session.get, call:str, call:dict, call:headers.pop, call:httpx.AsyncClient, call:request.body, call:client.request, call:logger.error, call:response_headers.pop, call:Response, raise:HTTPException | dep: logging, uuid, httpx, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.services.docker, src.services.shared.tunnel, src.schemas.tool, src.services.tool.instance_service
+- tool_lifecycle.py | FastAPI router providing REST endpoints for managing Docker-based tool instance lifecycle operations (start, stop, restart, delete). | exp: func:start_instance(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, data, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:start_tool_instance, raise:HTTPException, func:stop_instance(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:stop_tool_instance, raise:HTTPException, func:restart_instance(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, user_id, session) → dict, call:_get_user, call:_get_owned_project, call:restart_tool_instance, raise:HTTPException, func:delete_instance(project_id: uuid.UUID, repo_id: uuid.UUID, instance_id: uuid.UUID, force, user_id, session) → None, call:_get_user, call:_get_owned_project, call:delete_tool_instance, call:str, call:detail.lower, raise:HTTPException | dep: logging, uuid, fastapi, sqlalchemy.ext.asyncio, src.auth.dependencies, src.schemas.tool, src.services.tool.instance_service
+- tool_types.py | Defines FastAPI REST endpoints for CRUD operations on tool types with validation for Docker Compose, Dockerfile, and manifest definitions. | exp: func:_require_admin(user: User) → None, func:create_tool_type(data: ToolTypeCreate, user_id, session) → ToolType, call:_get_user, call:_require_admin, call:session.scalar, call:select(ToolType).where, call:ToolType, call:session.add, call:session.commit, call:session.refresh, raise:HTTPException, func:list_tool_types(user_id, session) → list[ToolType], call:_get_user, call:session.execute, call:select(ToolType).order_by, call:list, call:result.scalars().all, func:get_tool_type(tool_type_id: uuid.UUID, user_id, session) → ToolType, call:_get_user, call:session.get, raise:HTTPException, func:update_tool_type(tool_type_id: uuid.UUID, data: ToolTypeUpdate, user_id, session) → ToolType, call:_get_user, call:_require_admin, call:session.get, call:data.model_dump, call:update_data.get, call:validate_compose_yaml, call:check_port_exposed, call:validate_required_variables, call:update_data.items, call:setattr, call:session.commit, call:session.refresh, raise:HTTPException, func:validate_tool_type_template(data: ToolTypeValidateRequest, user_id, session) → dict, call:_get_user, call:errors.append, call:validate_compose_yaml, call:str, call:data.dockerfile_template.strip().startswith, call:len, func:validate_tool_type(tool_type_id: uuid.UUID, user_id, session) → dict, call:_get_user, call:session.get, call:errors.append, call:validate_compose_yaml, call:str, call:tool_type.dockerfile_template.strip().startswith, call:len, raise:HTTPException, func:delete_tool_type(tool_type_id: uuid.UUID, user_id, session) → None, call:_get_user, call:_require_admin, call:session.get, call:session.delete, call:session.commit, raise:HTTPException | dep: uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.api.tool.tool_types_validation, src.auth.dependencies, src.models, src.models.user, src.schemas.tool
+- tool_types_validation.py | Provides validation utilities for Docker Compose templates including YAML parsing, port exposure checking, and required template variable verification. | exp: func:sanitize_template_vars(template: str) → str, call:re.sub, func:validate_compose_yaml(template: str) → dict, call:sanitize_template_vars, call:yaml.safe_load, call:isinstance, raise:ValueError, func:check_port_exposed(parsed: dict, port: int) → bool, call:str, call:isinstance, call:parsed["services"].values, call:port_mapping.split, call:mapping.split, func:validate_required_variables(template: str, variables: list[str]) → None, raise:HTTPException | dep: re, yaml, fastapi
+## arch
+Modular FastAPI router pattern with domain-driven separation of concerns (types, instances, sessions, lifecycle) and Docker-centric validation/compilation utilities for container orchestration.
+## tags
+get, call:, tool, raise:httpexception, user, instance, call:str, call:session.get
+## symbols
+- CreateToolDefinitionRequest
+- UpdateToolDefinitionRequest
+- get_user_sessions
+- create_tool_definition
+- list_tool_definitions
+- get_tool_definition
+- update_tool_definition
+- delete_tool_definition
+## workflows
+- change tool behavior
+  read: __init__.py, sessions.py, tool_definitions.py
+## dirty
+-

apps/api/src/api/tool/__init__.py

@@ -0,0 +1,15 @@
+"""Tool API routers module."""
+
+from src.api.tool.sessions import sessions_router
+from src.api.tool.tool_definitions import router as tool_definitions_router
+from src.api.tool.tool_instances import router as tool_instances_router
+from src.api.tool.tool_lifecycle import router as tool_lifecycle_router
+from src.api.tool.tool_types import router as tool_types_router
+
+__all__ = [
+    "sessions_router",
+    "tool_definitions_router",
+    "tool_instances_router",
+    "tool_lifecycle_router",
+    "tool_types_router",
+]

apps/api/src/api/tool/sessions.py

@@ -0,0 +1,86 @@
+"""Sessions API endpoints (running instances for current user)."""
+
+import uuid
+
+from fastapi import APIRouter, Depends
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
+from src.models import GitRepository
+from src.models import Project
+from src.models import ToolInstance
+from src.models import ToolType
+
+sessions_router = APIRouter(prefix="/users", tags=["sessions"])
+
+
+@sessions_router.get(
+    "/me/sessions",
+    summary="Get user sessions",
+    description="Get all active sessions (running instances) for the current user.",
+)
+async def get_user_sessions(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get all active sessions for the current user.
+
+    Args:
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Dictionary containing list of active sessions with instance details.
+    """
+    _user = await _get_user(session, user_id)
+
+    result = await session.execute(
+        select(ToolInstance)
+        .where(ToolInstance.owner_id == user_id)
+        .where(
+            ToolInstance.status.in_(
+                ["running", "building", "pending", "stopped", "error"]
+            )
+        )
+        .order_by(ToolInstance.created_at.desc())
+    )
+    instances = result.scalars().all()
+
+    sessions = []
+    for instance in instances:
+        tool_type = await session.get(ToolType, instance.tool_type_id)
+        repo = await session.get(GitRepository, instance.repository_id)
+        project = await session.get(Project, instance.project_id)
+
+        workspace_name = None
+        if instance.workspace_id:
+            from src.models import Workspace as WorkspaceModel
+            workspace = await session.get(WorkspaceModel, instance.workspace_id)
+            if workspace:
+                workspace_name = workspace.name
+
+        sessions.append(
+            {
+                "id": str(instance.id),
+                "display_name": instance.display_name,
+                "tool_type_name": tool_type.name if tool_type else "unknown",
+                "tool_icon": tool_type.name if tool_type else "code",
+                "tool_type_interfaces": [tool_type.interface_type] if tool_type else [],
+                "repository_name": repo.name if repo else "unknown",
+                "repository_id": str(instance.repository_id),
+                "project_name": project.name if project else "unknown",
+                "project_id": str(instance.project_id),
+                "workspace_name": workspace_name,
+                "status": instance.status,
+                "url": instance.url,
+                "selected_config_profile_id": str(instance.selected_config_profile_id)
+                if instance.selected_config_profile_id
+                else None,
+                "created_at": instance.created_at.isoformat()
+                if instance.created_at
+                else None,
+            }
+        )
+
+    return {"sessions": sessions}