fix(terminal): prioritize selected copy menu

Handle selected-output context menus during capture so xterm and the browser cannot open a competing menu.
merge: add terminal right click copy action
2026-07-22 14:25:20 +02:00 · 2026-07-22 14:15:47 +02:00 · 2026-07-22 14:15:46 +02:00 · 2026-07-22 13:01:32 +02:00 · 2026-07-22 13:01:31 +02:00 · 2026-07-22 12:52:20 +02:00
1207 changed files with 49385 additions and 19854 deletions
@@ -1,3 +1,3 @@
 {
-  "fingerprint": "c36b11ec5edebc02aa51b1113a7a11dc2559e812"
+  "fingerprint": "e7b3130f52a328d4051e75364e5394ac63df60c6"
 }
@@ -2,13 +2,12 @@
 <!-- Auto-generated by gentle-pi extensions/skill-registry.ts. Run /skill-registry:refresh to regenerate. -->
-Last updated: 2026-06-02
+Last updated: 2026-06-17
 ## Sources scanned
 - .opencode/skills
 - .claude/skills
 - /home/alex/.config/opencode/skills
 ## Contract
@@ -20,12 +19,11 @@ Last updated: 2026-06-02
 | Skill | Trigger / description | Scope | Path |
 | --- | --- | --- | --- |
-| `auto-commit` | Use when you are making multiple edits or completing significant work in a git repository to automatically create commits | user | `/home/alex/.config/opencode/skills/auto-commit/SKILL.md` |
+| `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-apply-change` | Implement tasks from an OpenSpec change. Use when the user wants to start implementing, continue implementation, or work through tasks. | project | `/home/alex/projects/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-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/alex/projects/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-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/alex/projects/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` |
-| `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/alex/projects/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` |
 | `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/alex/projects/headquarter/.claude/skills/sift-backlog/SKILL.md` |
 ## Loading protocol
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -17,6 +17,7 @@ __pycache__/
 *.so
 .python-version
 .venv/
 .venv-test/
 venv/
 env/
 .pytest_cache/
@@ -54,3 +55,6 @@ Thumbs.db
 .atl/
 .sisyphus/
 .pi-lens/
 minerv3/
 .cache/
 openspec-audit-report.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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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/
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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")
@@ -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")
@@ -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
@@ -232,20 +232,6 @@ def upgrade() -> None:
                            "writable": True,
                            "owner": "user",
                        },
                        {
                            "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"],
@@ -322,10 +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
@@ -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,
    )
@@ -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")
@@ -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)
@@ -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)
@@ -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)
@@ -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
@@ -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,
        },
    )
@@ -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
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -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
 -
@@ -1,6 +1 @@
-from src.api.auth import router as auth_router
+"""API routers package."""
 from src.api.events import router as events_router
 from src.api.notifications import router as notifications_router
 from src.api.users import router as users_router
 __all__ = ["auth_router", "events_router", "notifications_router", "users_router"]
@@ -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
 -
@@ -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
 -
@@ -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"]
@@ -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)
@@ -2,12 +2,12 @@ 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__)
@@ -38,28 +38,6 @@ async def _get_or_create_config(
    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
    notification_mute_categories: list[str] | None = None
    notification_toast_level: 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
    notification_mute_categories: list[str] | None = None
    notification_toast_level: str | None = None
@router.get(
    "/config",
    response_model=UserConfigResponse,
@@ -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
 -
@@ -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"]
@@ -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))
@@ -3,7 +3,6 @@ import shutil
 import uuid
 from fastapi import APIRouter, Depends, HTTPException, Response, status
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession
@@ -13,38 +12,20 @@ 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
-from src.models.tool_instance import ToolInstance
+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,
@@ -101,7 +82,7 @@ async def list_projects(
    )
    projects = result.scalars().all()
-    from src.models.workspace import Workspace
+    from src.models import Workspace
    enriched = []
    for project in projects:
@@ -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
 -
@@ -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
 -
@@ -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",
 ]
@@ -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"])
@@ -10,7 +10,7 @@ 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.event_bus import InstanceEventBus, InstanceEventPayload
+from src.services.instance.event_bus import InstanceEventBus, InstanceEventPayload
 router = APIRouter(prefix="/events", tags=["events"])
@@ -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,
@@ -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 import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import ToolType
 logger = logging.getLogger(__name__)
@@ -9,8 +9,8 @@ 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.user_config import UserConfig
+from src.models import UserConfig
-from src.services.notification_service import notification_service
+from src.services.shared.notification_service import notification_service
 router = APIRouter(prefix="/notifications", tags=["notifications"])
@@ -3,6 +3,8 @@
 import asyncio
 import json
 import logging
 from asyncio import QueueFull
 from json import JSONDecodeError
 import uuid
 from contextlib import suppress
@@ -12,14 +14,28 @@ 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.terminal_session import TerminalSessionModel
+from src.models import (
-from src.models.tool_instance import ToolInstance
+    TerminalSessionModel,
-from src.models.tool_type import ToolType
+    ToolDefinitionManifest,
-from src.services.terminal_manager import MaxSessionsExceededError, terminal_manager
+    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."""
@@ -57,6 +73,39 @@ async def terminal_websocket_specific(
    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,
@@ -139,7 +188,7 @@ async def _handle_terminal_websocket(
        )
        return
-    # Fetch tool type to get startup_command
+    # 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:
@@ -149,6 +198,14 @@ async def _handle_terminal_websocket(
            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
@@ -159,6 +216,7 @@ async def _handle_terminal_websocket(
                instance_uuid,
                instance.container_id,
                startup_command=startup_command,
                container_user=container_user,
            )
            slot_session_id = "default"
        else:
@@ -189,6 +247,7 @@ async def _handle_terminal_websocket(
                        startup_command=startup_command,
                        name=db_row.name,
                        session_id=target_session_id,
                        container_user=container_user,
                    )
                else:
                    logger.warning(
@@ -266,8 +325,38 @@ async def _handle_terminal_websocket(
                )
 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:
-    """Read input from WebSocket and send to container."""
+    """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
@@ -277,72 +366,100 @@ async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> N
            message = await websocket.receive()
            if message["type"] == "websocket.receive":
                if "bytes" in message:
-                    await session.write_input(message["bytes"])
+                    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("{"):
                        # Control message (JSON)
                        try:
-                            ctrl = json.loads(text)
+                            parsed = json.loads(text)
-                            msg_type = ctrl.get("type")
+                        except JSONDecodeError:
                            parsed = None
                        if isinstance(parsed, dict) and "type" in parsed:
                            ctrl = parsed
-                            if msg_type == "resize":
+                    if ctrl is None:
-                                cols = ctrl.get("cols", 80)
+                        if not _queue_terminal_input(
-                                rows = ctrl.get("rows", 24)
+                            input_queue, session, text.encode("utf-8")
-                                logger.debug(
+                        ):
-                                    "Received resize message for instance %s: %sx%s",
+                            logger.warning(
-                                    instance_id,
+                                "Terminal input buffer exceeded for %s", instance_id
-                                    cols,
+                            )
-                                    rows,
+                            await websocket.close(
-                                )
+                                code=1009, reason="Terminal input buffer full"
-                                await session.resize(cols, rows)
+                            )
-                            elif msg_type == "ack":
+                            break
-                                char_count = ctrl.get("chars", 0)
+                        continue
                                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
+                    msg_type = ctrl["type"]
-                                new_session = await terminal_manager.reset_session(
+                    if msg_type == "resize":
-                                    session.instance_id,
+                        cols = ctrl.get("cols", 80)
-                                    session.container_id,
+                        rows = ctrl.get("rows", 24)
-                                    startup_command=session.startup_command,
+                        logger.debug(
-                                    session_id=session_ref.slot_session_id,
+                            "Received resize message for instance %s: %sx%s",
-                                    name=session.name,
+                            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"}
                        )
-                                # Update the mutable session reference
+                        # Reset the session scoped to its slot
-                                session_ref.session = new_session
+                        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,
                        )
-                                # Attach to new session
+                        # Update the mutable session reference
-                                await terminal_manager.attach_websocket(
+                        session_ref.session = new_session
                                    new_session, websocket
                                )
                                await websocket.send_json(
                                    {"type": "status", "status": "connected"}
                                )
-                                # Continue the loop with the new session
+                        # Attach to new session
-                                continue
+                        await terminal_manager.attach_websocket(new_session, websocket)
                        await websocket.send_json(
                            {"type": "status", "status": "connected"}
                        )
-                        except json.JSONDecodeError:
+                        # Continue the loop with the new session
-                            # Not a valid JSON control message, treat as regular input
+                        continue
                            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:
+    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:
@@ -486,6 +603,7 @@ async def create_terminal_session(
    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(
@@ -493,6 +611,7 @@ async def create_terminal_session(
            instance.container_id,
            startup_command=startup_command,
            name=name,
            container_user=container_user,
        )
    except MaxSessionsExceededError:
        raise HTTPException(
@@ -595,6 +714,7 @@ async def reset_specific_terminal_session(
    # 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,
@@ -602,6 +722,7 @@ async def reset_specific_terminal_session(
        startup_command=startup_command,
        session_id=key[1],
        name=name,
        container_user=container_user,
    )
    return {
@@ -687,6 +808,7 @@ async def reset_terminal_session(
    # 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
@@ -694,6 +816,7 @@ async def reset_terminal_session(
            instance_id,
            instance.container_id,
            startup_command=startup_command,
            container_user=container_user,
        )
        logger.info(
@@ -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
 -
@@ -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
 -
@@ -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",
 ]
@@ -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}
@@ -9,9 +9,9 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_definition_manifest import ToolDefinitionManifest
+from src.models import ToolDefinitionManifest
-from src.models.tool_type import ToolType
+from src.models import ToolType
-from src.services.manifest_compiler import (
+from src.services.build.manifest_compiler import (
    compile_compose,
    compile_dockerfile,
    compile_entrypoint,
@@ -173,7 +173,7 @@ async def list_tool_definitions(
    """
    query = select(ToolDefinitionManifest)
    if not include_bases:
-        query = query.where(ToolDefinitionManifest.is_base == False)
+        query = query.where(ToolDefinitionManifest.is_base.is_(False))
    result = await session.execute(
        query.order_by(ToolDefinitionManifest.created_at.desc())
@@ -0,0 +1,419 @@
 """Tool instance API endpoints."""
 import logging
 import uuid
 import httpx
 from fastapi import (
    APIRouter,
    Depends,
    HTTPException,
    Request,
    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 ToolInstance
 from src.services.docker import get_container_logs, get_container_status
 from src.services.shared.tunnel import check_tunnel_health
 from src.schemas.tool import CreateInstanceRequest
 from src.services.tool.instance_service import (
    create_tool_instance,
    recreate_instance_tunnel,
    rename_tool_instance,
 )
 logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/projects", tags=["tool-instances"])
@router.post(
    "/{project_id}/repositories/{repo_id}/instances",
    summary="Create tool instance",
    description="Create a new tool instance for a repository.",
 )
 async def create_instance(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    data: CreateInstanceRequest,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    try:
        instance = await create_tool_instance(session, user_id, project_id, repo_id, data)
    except ValueError as exc:
        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
    except RuntimeError as exc:
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
        )
    return {
        "id": str(instance.id),
        "name": instance.name,
        "display_name": instance.display_name,
        "tool_type_id": str(instance.tool_type_id),
        "status": instance.status,
        "workspace_id": str(instance.workspace_id) if instance.workspace_id else None,
        "selected_config_profile_id": str(instance.selected_config_profile_id) if instance.selected_config_profile_id else None,
        "created_at": instance.created_at.isoformat(),
    }
@router.get(
    "/{project_id}/repositories/{repo_id}/instances",
    summary="List instances",
    description="List all tool instances for a repository.",
 )
 async def list_instances(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> list[dict]:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    result = await session.execute(
        select(ToolInstance)
        .where(ToolInstance.repository_id == repo_id)
        .where(ToolInstance.owner_id == user_id)
        .order_by(ToolInstance.created_at.desc())
    )
    instances = result.scalars().all()
    return [
        {"id": str(i.id), "name": i.name, "display_name": i.display_name,
         "tool_type_id": str(i.tool_type_id), "status": i.status, "url": i.url,
         "port": i.port, "container_id": i.container_id,
         "created_at": i.created_at.isoformat() if i.created_at else None}
        for i in instances
    ]
@router.get(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}",
    summary="Get instance",
    description="Get details for a specific tool instance.",
 )
 async def get_instance(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    instance = await session.get(ToolInstance, instance_id)
    if instance is None or instance.repository_id != repo_id:
        raise HTTPException(
            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
        )
    docker_status = None
    if instance.container_id:
        docker_status = get_container_status(instance.container_id)
    return {
        "id": str(instance.id),
        "name": instance.name,
        "display_name": instance.display_name,
        "tool_type_id": str(instance.tool_type_id),
        "status": instance.status,
        "url": instance.url,
        "public_url": instance.public_url,
        "port": instance.port,
        "container_id": instance.container_id,
        "container_name": instance.container_name,
        "compose_path": instance.compose_path,
        "workspace_id": str(instance.workspace_id) if instance.workspace_id else None,
        "selected_config_profile_id": str(instance.selected_config_profile_id) if instance.selected_config_profile_id else None,
        "ssh_key_ids": instance.ssh_key_ids,
        "created_at": instance.created_at.isoformat() if instance.created_at else None,
        "last_started_at": instance.last_started_at.isoformat() if instance.last_started_at else None,
        "docker_status": docker_status,
    }
@router.patch(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}",
    summary="Rename instance",
    description="Update the display name of a tool instance.",
 )
 async def rename_instance(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    data: dict,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    display_name = data.get("display_name", "").strip()
    if not display_name:
        raise HTTPException(
            status_code=status.HTTP_400_BAD_REQUEST,
            detail="display_name is required",
        )
    try:
        instance = await rename_tool_instance(
            session, user_id, project_id, repo_id, instance_id, display_name
        )
    except ValueError as exc:
        raise HTTPException(
            status_code=status.HTTP_404_NOT_FOUND, detail=str(exc)
        )
    return {
        "id": str(instance.id),
        "name": instance.name,
        "display_name": instance.display_name,
    }
@router.get(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/logs",
    summary="Get instance logs",
    description="Get container logs for a tool instance.",
 )
 async def get_instance_logs(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    tail: int = 100,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    instance = await session.get(ToolInstance, instance_id)
    if instance is None or instance.repository_id != repo_id:
        raise HTTPException(
            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
        )
    if not instance.container_id:
        return {"logs": "No container running"}
    logs = get_container_logs(instance.container_id, tail)
    return {"logs": logs}
@router.post(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/recreate-tunnel",
    summary="Recreate tunnel",
    description="Recreate the temporary Cloudflare tunnel for a running instance.",
 )
 async def recreate_tunnel_endpoint(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    try:
        return await recreate_instance_tunnel(
            session, user_id, project_id, repo_id, instance_id
        )
    except ValueError as exc:
        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
    except RuntimeError as exc:
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
        )
@router.get(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/health",
    summary="Check instance health",
    description="Check container and tunnel health for an instance.",
 )
 async def check_instance_tunnel_health(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    instance = await session.get(ToolInstance, instance_id)
    if instance is None or instance.repository_id != repo_id:
        raise HTTPException(
            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
        )
    container_info = {"status": "not_found", "exit_code": None, "health": None}
    if instance.container_id:
        container_info = get_container_status(instance.container_id)
    response = {
        "healthy": False,
        "container_status": container_info["status"],
        "container_health": container_info["health"],
        "tunnel_status": "not_applicable",
        "tunnel_status_code": None,
        "probe_status": "not_applicable",
        "last_probe_output": None,
        "error": None,
    }
    if instance.status == "probing":
        response["probe_status"] = "pending"
    elif instance.probe_result:
        response["probe_status"] = "success" if instance.probe_result.get("success") else "failed"
        response["last_probe_output"] = "\n".join(instance.probe_result.get("logs", []))
    if instance.url and instance.status in ("running", "unhealthy"):
        tunnel_health = check_tunnel_health(instance.url)
        response["tunnel_status"] = tunnel_health["tunnel_status"]
        response["tunnel_status_code"] = tunnel_health.get("status_code")
        if tunnel_health.get("error"):
            response["error"] = tunnel_health["error"]
    container_healthy = container_info["status"] == "running"
    if instance.url:
        response["healthy"] = container_healthy and response["tunnel_status"] == "healthy"
    else:
        response["healthy"] = container_healthy
    if not container_healthy:
        response["error"] = f"Container is {container_info['status']}"
        if container_info["exit_code"] is not None:
            response["error"] += f" (exit code: {container_info['exit_code']})"
    return response
@router.get(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/events",
    summary="Get instance events history",
    description="Get lifecycle event history for a tool instance.",
 )
 async def get_instance_events(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    limit: int = 50,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> list[dict]:
    from sqlalchemy import select
    from src.models import InstanceEvent
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    instance = await session.get(ToolInstance, instance_id)
    if instance is None or instance.repository_id != repo_id:
        raise HTTPException(
            status_code=status.HTTP_404_NOT_FOUND, detail="instance not found"
        )
    result = await session.execute(
        select(InstanceEvent)
        .where(InstanceEvent.instance_id == instance_id)
        .order_by(InstanceEvent.created_at.desc())
        .limit(limit)
    )
    rows = result.scalars().all()
    return [
        {
            "id": str(row.id),
            "event_type": row.event_type,
            "status": row.status,
            "message": row.message,
            "metadata": row.event_metadata,
            "created_at": row.created_at.isoformat() if row.created_at else None,
        }
        for row in rows
    ]
@router.api_route(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/proxy/{path:path}",
    methods=["GET", "POST", "PUT", "DELETE", "PATCH", "HEAD", "OPTIONS"],
    summary="Proxy to instance",
    description="Proxy HTTP requests to a running tool instance.",
 )
 async def proxy_to_instance(
    request: Request,
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    path: str = "",
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> Response:
    instance = await session.get(ToolInstance, instance_id)
    if instance is None or instance.repository_id != repo_id:
        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_name:
        raise HTTPException(
            status_code=status.HTTP_503_SERVICE_UNAVAILABLE,
            detail="instance is not running",
        )
    target_url = f"http://{instance.container_name}:{instance.port}"
    if path:
        target_url += f"/{path}"
    query_string = str(request.query_params)
    if query_string:
        target_url += f"?{query_string}"
    headers = dict(request.headers)
    headers.pop("host", None)
    headers.pop("cookie", None)
    try:
        async with httpx.AsyncClient() as client:
            body = await request.body()
            response = await client.request(
                method=request.method,
                url=target_url,
                headers=headers,
                content=body,
                follow_redirects=False,
                timeout=30.0,
            )
    except Exception as exc:
        logger.error("Proxy error: %s", exc)
        raise HTTPException(
            status_code=status.HTTP_502_BAD_GATEWAY,
            detail=f"failed to reach instance: {exc}",
        )
    response_headers = dict(response.headers)
    for header in ["content-encoding", "transfer-encoding", "connection"]:
        response_headers.pop(header, None)
    return Response(
        content=response.content,
        status_code=response.status_code,
        headers=response_headers,
    )
@@ -0,0 +1,135 @@
 """Tool instance lifecycle API endpoints."""
 import logging
 import uuid
 from fastapi import APIRouter, Depends, HTTPException, status
 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.schemas.tool import StartInstanceRequest
 from src.services.tool.instance_service import (
    delete_tool_instance,
    restart_tool_instance,
    start_tool_instance,
    stop_tool_instance,
 )
 logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/projects", tags=["tool-instances"])
@router.post(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/start",
    summary="Start instance",
    description="Start a tool instance using Docker Compose.",
 )
 async def start_instance(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    data: StartInstanceRequest | None = None,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    try:
        return await start_tool_instance(
            session, user_id, project_id, repo_id, instance_id, data
        )
    except ValueError as exc:
        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
    except RuntimeError as exc:
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
        )
@router.post(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/stop",
    summary="Stop instance",
    description="Stop a running tool instance.",
 )
 async def stop_instance(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    try:
        return await stop_tool_instance(session, user_id, project_id, repo_id, instance_id)
    except ValueError as exc:
        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=str(exc))
@router.post(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/restart",
    summary="Restart instance",
    description="Restart a tool instance.",
 )
 async def restart_instance(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    try:
        return await restart_tool_instance(
            session, user_id, project_id, repo_id, instance_id
        )
    except ValueError as exc:
        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
    except RuntimeError as exc:
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
        )
@router.delete(
    "/{project_id}/repositories/{repo_id}/instances/{instance_id}",
    summary="Delete instance",
    description="Delete a tool instance and remove its Docker containers and files.",
 )
 async def delete_instance(
    project_id: uuid.UUID,
    repo_id: uuid.UUID,
    instance_id: uuid.UUID,
    force: bool = False,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> None:
    _user = await _get_user(session, user_id)
    _project = await _get_owned_project(project_id, user_id, session)
    try:
        await delete_tool_instance(
            session, user_id, project_id, repo_id, instance_id, force
        )
    except ValueError as exc:
        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=str(exc))
    except RuntimeError as exc:
        detail = str(exc)
        if "uncommitted changes" in detail.lower():
            raise HTTPException(
                status_code=status.HTTP_409_CONFLICT,
                detail={
                    "message": "Repository has uncommitted changes",
                    "changed_files": detail,
                    "force_required": True,
                },
            )
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=detail
        )
@@ -1,19 +1,23 @@
 import uuid
 from datetime import datetime
 from fastapi import APIRouter, Depends, HTTPException, status
 from pydantic import BaseModel, ConfigDict, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
-from src.api.tool_types_validation import (
+from src.api.tool.tool_types_validation import (
    check_port_exposed,
    validate_compose_yaml,
    validate_required_variables,
 )
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
-from src.models.tool_type import ToolType
+from src.models import ToolType
 from src.models.user import User
 from src.schemas.tool import (
    ToolTypeCreate,
    ToolTypeResponse,
    ToolTypeUpdate,
    ToolTypeValidateRequest,
 )
 router = APIRouter(prefix="/tool-types", tags=["tool-types"])
@@ -29,237 +33,6 @@ async def _require_admin(user: User) -> None:
    pass
 class ToolTypeCreate(BaseModel):
    name: str
    display_name: str
    description: str | None = None
    default_port: int = 0
    definition_type: str = "compose"
    manifest_id: uuid.UUID | None = None
    compose_template: str | None = None
    dockerfile_template: str | None = None
    build_context: dict | None = None
    readiness_probe: dict | None = None
    startup_command: str | None = None
    required_variables: list[str] = []
    category: str = "other"
    interface_type: str = "web"
    requires_port: bool = True
    @field_validator("definition_type")
    @classmethod
    def validate_definition_type(cls, v: str) -> str:
        if v not in ("compose", "dockerfile", "manifest"):
            raise ValueError(
                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
            )
        return v
    @field_validator("compose_template")
    @classmethod
    def validate_compose_template(cls, v: str | None, info) -> str | None:
        data = info.data
        if data.get("definition_type") != "compose":
            return v
        if v is None or not v.strip():
            raise ValueError(
                "compose_template is required when definition_type is 'compose'"
            )
        validate_compose_yaml(v)
        return v
    @field_validator("dockerfile_template")
    @classmethod
    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
        data = info.data
        if data.get("definition_type") != "dockerfile":
            return v
        if v is None or not v.strip():
            raise ValueError(
                "dockerfile_template is required when definition_type is 'dockerfile'"
            )
        if not v.strip().startswith("FROM"):
            raise ValueError("Dockerfile must start with a FROM instruction")
        return v
    @field_validator("interface_type")
    @classmethod
    def validate_interface_type(cls, v: str) -> str:
        if v not in ("web", "terminal"):
            raise ValueError("interface_type must be 'web' or 'terminal'")
        return v
    @field_validator("default_port")
    @classmethod
    def validate_default_port(cls, v: int, info) -> int:
        data = info.data
        requires_port = data.get("requires_port", True)
        if not requires_port:
            return v
        if v <= 0 or v > 65535:
            raise ValueError("Port must be between 1 and 65535")
        return v
    @field_validator("required_variables")
    @classmethod
    def validate_required_variables(cls, v: list[str], info) -> list[str]:
        if not v:
            return v
        data = info.data
        if data.get("definition_type") != "compose":
            return v
        template = data.get("compose_template")
        if not template:
            return v
        for var in v:
            placeholder = f"{{{{{var}}}}}"
            if placeholder not in template:
                raise ValueError(
                    f"Required variable '{var}' not found in compose template"
                )
        return v
    @model_validator(mode="after")
    def validate_templates(self) -> "ToolTypeCreate":
        if self.definition_type == "manifest":
            if self.manifest_id is None:
                raise ValueError(
                    "manifest_id is required when definition_type is 'manifest'"
                )
            return self
        if self.definition_type == "dockerfile" and (
            self.dockerfile_template is None or not self.dockerfile_template.strip()
        ):
            raise ValueError(
                "dockerfile_template is required when definition_type is 'dockerfile'"
            )
        if self.definition_type == "compose" and (
            self.compose_template is None or not self.compose_template.strip()
        ):
            raise ValueError(
                "compose_template is required when definition_type is 'compose'"
            )
        # Validate that default_port is exposed in compose template (only if requires_port)
        if (
            self.requires_port
            and self.definition_type == "compose"
            and self.compose_template
        ):
            try:
                parsed = validate_compose_yaml(self.compose_template)
            except ValueError:
                return self
            if not check_port_exposed(parsed, self.default_port):
                raise ValueError(
                    f"Port {self.default_port} is not exposed in the compose template. Add it to the 'ports' section."
                )
        return self
 class ToolTypeUpdate(BaseModel):
    display_name: str | None = None
    description: str | None = None
    default_port: int | None = None
    definition_type: str | None = None
    manifest_id: uuid.UUID | None = None
    compose_template: str | None = None
    dockerfile_template: str | None = None
    build_context: dict | None = None
    readiness_probe: dict | None = None
    startup_command: str | None = None
    required_variables: list[str] | None = None
    category: str | None = None
    interface_type: str | None = None
    requires_port: bool | None = None
    @field_validator("definition_type")
    @classmethod
    def validate_definition_type(cls, v: str | None) -> str | None:
        if v is None:
            return v
        if v not in ("compose", "dockerfile", "manifest"):
            raise ValueError(
                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
            )
        return v
    @field_validator("interface_type")
    @classmethod
    def validate_interface_type(cls, v: str | None) -> str | None:
        if v is None:
            return v
        if v not in ("web", "terminal"):
            raise ValueError("interface_type must be 'web' or 'terminal'")
        return v
    @field_validator("compose_template")
    @classmethod
    def validate_compose_template(cls, v: str | None, info) -> str | None:
        if v is None:
            return v
        data = info.data
        definition_type = data.get("definition_type")
        if definition_type and definition_type != "compose":
            return v
        validate_compose_yaml(v)
        return v
    @field_validator("dockerfile_template")
    @classmethod
    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
        if v is None:
            return v
        data = info.data
        definition_type = data.get("definition_type")
        if definition_type and definition_type != "dockerfile":
            return v
        if not v.strip().startswith("FROM"):
            raise ValueError("Dockerfile must start with a FROM instruction")
        return v
 class ToolTypeResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)
    id: uuid.UUID
    name: str
    display_name: str
    description: str | None
    category: str
    interface_type: str
    requires_port: bool
    default_port: int
    definition_type: str
    manifest_id: uuid.UUID | None
    compose_template: str | None
    dockerfile_template: str | None
    build_context: dict | None
    readiness_probe: dict | None
    startup_command: str | None
    required_variables: list[str]
    created_by_id: uuid.UUID | None
    created_at: datetime
    updated_at: datetime
@router.post(
    "",
    response_model=ToolTypeResponse,
@@ -461,12 +234,6 @@ async def update_tool_type(
    return tool_type
 class ToolTypeValidateRequest(BaseModel):
    definition_type: str
    compose_template: str | None = None
    dockerfile_template: str | None = None
@router.post(
    "/validate",
    summary="Validate tool type template",
@@ -60,8 +60,14 @@ def check_port_exposed(parsed: dict, port: int) -> bool:
    for service_config in parsed["services"].values():
        if isinstance(service_config, dict) and "ports" in service_config:
            for port_mapping in service_config["ports"]:
-                if isinstance(port_mapping, str) and port_str in port_mapping:
+                if isinstance(port_mapping, str):
-                    return True
+                    # Port mappings can be "host:container", "ip:host:container",
                    # "container", or ".../protocol". The container port is the
                    # last numeric segment before any protocol suffix.
                    mapping = port_mapping.split("/")[0]
                    parts = mapping.split(":")
                    if parts[-1] == port_str:
                        return True
                elif isinstance(port_mapping, int) and port_mapping == port:
                    return True
@@ -0,0 +1,23 @@
 # apps/api/src/api/user (index)
 dir: apps/api/src/api/user
 ## role
 Provides user-facing API endpoints for authentication, profile management, and SSH key operations in the FastAPI backend.
 ## parent
 index: apps/api/src/api/.pi-map.index.md
 map: apps/api/src/api/.pi-map.md
 ## children
 -
 ## files
 - __init__.py
 - auth.py
 - ssh_keys.py
 - users.py
 ## links
 index: apps/api/src/api/user/.pi-map.index.md
 map: apps/api/src/api/user/.pi-map.md
 ## workflows
 - change user behavior
  read: __init__.py, auth.py, ssh_keys.py
 ## dirty
 -
@@ -0,0 +1,30 @@
 # apps/api/src/api/user
 dir: apps/api/src/api/user
 index: apps/api/src/api/user/.pi-map.index.md
 ## role
 Provides user-facing API endpoints for authentication, profile management, and SSH key operations in the FastAPI backend.
 ## files
 - __init__.py | Aggregates and exports user-related API routers from submodules for easy importing. | dep: src.api.user.auth, src.api.user.ssh_keys, src.api.user.users
 - auth.py | Implements OAuth2/OIDC authentication endpoints for a FastAPI application using Authentik as the identity provider, including login initiation, callback handling, session management, logout, and current user retrieval. | exp: func:get_db_session() → AsyncGenerator[AsyncSession, None], call:SessionLocal, func:login(next) → RedirectResponse, call:Settings, call:token_urlsafe, call:build_login_redirect_url, call:logger.debug, call:RedirectResponse, call:response.set_cookie, func:callback(code: str, state: str, auth_state, auth_next, session) → RedirectResponse, call:logger.debug, call:logger.warning, call:Settings, call:httpx.AsyncClient, call:exchange_code_for_tokens, call:logger.info, call:logger.error, call:fetch_user_info, call:str, call:user_info.get, call:session.scalar, call:select(User).where, call:User, call:session.add, call:session.commit, call:session.refresh, call:create_session_cookie, call:build_cookie_options, call:cast, call:bool, call:cookie_options.get, call:RedirectResponse, call:redirect_response.set_cookie, call:redirect_response.delete_cookie, raise:HTTPException, func:logout(response: Response) → dict[str, str], call:Settings, call:build_cookie_options, call:cast, call:bool, call:str, call:cookie_options.get, call:response.delete_cookie, func:me(session_cookie, session) → dict[str, Any], call:logger.debug, call:bool, call:logger.warning, call:Settings, call:decode_session_cookie, call:session.get, call:logger.info, call:str, raise:HTTPException | dep: logging, secrets, typing, httpx, fastapi, fastapi.responses, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.cookies, src.auth.oidc, src.auth.session, src.config, src.database, src.models.user
 - ssh_keys.py | FastAPI router for managing Ed25519 SSH keys including generation, storage with encrypted private keys, signing payloads, and signature verification | exp: func:_get_fernet() → Fernet, call:Settings, call:hashlib.sha256(settings.session_secret.encode()).digest, call:settings.session_secret.encode, call:base64.urlsafe_b64encode, call:Fernet, func:generate_ssh_key_pair() → tuple[str, str], call:Ed25519PrivateKey.generate, call:private_key.public_key, call:private_key.private_bytes, call:serialization.NoEncryption, call:public_key.public_bytes, call:private_bytes.decode, call:public_bytes.decode, func:create_ssh_key(data: SSHKeyCreate, user_id, session) → SSHKey, call:_get_user, call:generate_ssh_key_pair, call:_get_fernet, call:fernet.encrypt(private_key.encode()).decode, call:private_key.encode, call:SSHKey, call:session.add, call:session.commit, call:session.refresh, func:list_ssh_keys(user_id, session) → list[SSHKey], call:_get_user, call:session.execute, call:select(SSHKey).where, call:list, call:result.scalars().all, func:delete_ssh_key(key_id: uuid.UUID, user_id, session) → None, call:_get_user, call:session.get, call:session.delete, call:session.commit, raise:HTTPException, func:sign_payload(key_id: uuid.UUID, data: SignPayloadRequest, user_id, session) → SignatureResponse, call:_get_user, call:session.get, call:_get_fernet, call:fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode, call:ssh_key.private_key_encrypted.encode, call:serialization.load_ssh_private_key, call:private_key_pem.encode, call:private_key.sign, call:data.payload.encode, call:SignatureResponse, call:base64.b64encode(signature).decode, raise:HTTPException, func:verify_signature(key_id: uuid.UUID, data: VerifySignatureRequest, user_id, session) → VerifySignatureResponse, call:_get_user, call:session.get, call:serialization.load_ssh_public_key, call:ssh_key.public_key.encode, call:base64.b64decode, call:public_key.verify, call:data.payload.encode, call:VerifySignatureResponse, raise:HTTPException | dep: base64, uuid, cryptography.fernet, cryptography.hazmat.primitives, cryptography.hazmat.primitives.asymmetric.ed25519, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.config, src.models, src.schemas.project, hashlib, cryptography
 - users.py | Implements FastAPI endpoints for user profile management including retrieval, updates, and avatar uploads with file validation. | exp: func:get_profile(user_id, session) → User, call:_get_user, func:update_profile(data: UserProfileUpdate, user_id, session) → User, call:_get_user, call:len, call:data.name.strip, call:data.email.strip, call:session.commit, call:session.refresh, raise:HTTPException, func:upload_avatar(file: UploadFile, user_id, session) → User, call:_get_user, call:file.read, call:len, call:Path, call:old_path.exists, call:old_path.unlink, call:filename_part.split(".")[-1].lower, call:uuid.uuid4, call:file_path.write_bytes, call:session.commit, call:session.refresh, raise:HTTPException | dep: uuid, pathlib, fastapi, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models.user, src.schemas.user, sqlalchemy
 ## arch
 Modular FastAPI router pattern with separate submodules for distinct concerns (auth, profile, SSH keys), using OAuth2/OIDC external identity provider (Authentik), encrypted key storage, and file upload handling.
 ## tags
 user, get, call:, key, ssh, src, cookie, raise:httpexception
 ## symbols
 - get_db_session
 - login
 - callback
 - logout
 - me
 - _get_fernet
 - generate_ssh_key_pair
 - create_ssh_key
 ## workflows
 - change user behavior
  read: __init__.py, auth.py, ssh_keys.py
 ## dirty
 -
@@ -0,0 +1,7 @@
 """User API routers module."""
 from src.api.user.auth import router as auth_router
 from src.api.user.ssh_keys import router as ssh_keys_router
 from src.api.user.users import router as users_router
 __all__ = ["auth_router", "ssh_keys_router", "users_router"]
@@ -1,18 +1,24 @@
 import base64
 import uuid
 from datetime import datetime
 from cryptography.fernet import Fernet
 from cryptography.hazmat.primitives import serialization
 from cryptography.hazmat.primitives.asymmetric.ed25519 import Ed25519PrivateKey
 from fastapi import APIRouter, Depends, HTTPException, status
 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.config import Settings
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
 from src.schemas.project import (
    SSHKeyCreate,
    SSHKeyResponse,
    SignPayloadRequest,
    SignatureResponse,
    VerifySignatureRequest,
    VerifySignatureResponse,
 )
 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
@@ -21,7 +27,7 @@ def _get_fernet() -> Fernet:
    """Generate a valid Fernet key from the session secret."""
    import base64
    import hashlib
-    
+
    settings = Settings()
    # Derive a 32-byte key from the session secret using SHA256
    key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
@@ -53,36 +59,6 @@ def generate_ssh_key_pair() -> tuple[str, str]:
    return private_bytes.decode("utf-8"), public_bytes.decode("utf-8")
 class SSHKeyCreate(BaseModel):
    name: str
 class SSHKeyResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)
    id: uuid.UUID
    name: str
    public_key: str
    created_at: datetime
 class SignPayloadRequest(BaseModel):
    payload: str
 class SignatureResponse(BaseModel):
    signature: str
 class VerifySignatureRequest(BaseModel):
    payload: str
    signature: str
 class VerifySignatureResponse(BaseModel):
    valid: bool
@router.post(
    "",
    response_model=SSHKeyResponse,
@@ -171,7 +147,9 @@ async def delete_ssh_key(
    user = await _get_user(session, user_id)
    ssh_key = await session.get(SSHKey, key_id)
    if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        raise HTTPException(
            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
        )
    await session.delete(ssh_key)
    await session.commit()
@@ -203,7 +181,9 @@ async def sign_payload(
    user = await _get_user(session, user_id)
    ssh_key = await session.get(SSHKey, key_id)
    if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        raise HTTPException(
            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
        )
    fernet = _get_fernet()
    private_key_pem = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
@@ -242,7 +222,9 @@ async def verify_signature(
    user = await _get_user(session, user_id)
    ssh_key = await session.get(SSHKey, key_id)
    if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
+        raise HTTPException(
            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
        )
    public_key = serialization.load_ssh_public_key(ssh_key.public_key.encode())
@@ -2,11 +2,11 @@ import uuid
 from pathlib import Path
 from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.user import User
 from src.schemas.user import UserProfileResponse, UserProfileUpdate
 router = APIRouter(prefix="/users", tags=["users"])
@@ -16,20 +16,6 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
 class UserProfileResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)
    id: uuid.UUID
    email: str
    name: str
    avatar_url: str | None
 class UserProfileUpdate(BaseModel):
    name: str | None = None
    email: str | None = None
@router.get(
    "/me",
    response_model=UserProfileResponse,
@@ -77,12 +63,16 @@ async def update_profile(
    if data.name is not None:
        if len(data.name.strip()) == 0:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="name cannot be empty")
+            raise HTTPException(
                status_code=status.HTTP_400_BAD_REQUEST, detail="name cannot be empty"
            )
        user.name = data.name.strip()
    if data.email is not None:
        if "@" not in data.email:
-            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid email")
+            raise HTTPException(
                status_code=status.HTTP_400_BAD_REQUEST, detail="invalid email"
            )
        user.email = data.email.strip()
    await session.commit()
@@ -0,0 +1,24 @@
 # apps/api/src/api/workspace (index)
 dir: apps/api/src/api/workspace
 ## role
 Provides REST API endpoints for managing user workspaces, including file operations, Git version control, tool instances, and workspace lifecycle management.
 ## parent
 index: apps/api/src/api/.pi-map.index.md
 map: apps/api/src/api/.pi-map.md
 ## children
 -
 ## files
 - __init__.py
 - workspace_files.py
 - workspace_git.py
 - workspace_instances.py
 - workspaces.py
 ## links
 index: apps/api/src/api/workspace/.pi-map.index.md
 map: apps/api/src/api/workspace/.pi-map.md
 ## workflows
 - change workspace behavior
  read: __init__.py, workspace_files.py, workspace_git.py
 ## dirty
 -
@@ -0,0 +1,31 @@
 # apps/api/src/api/workspace
 dir: apps/api/src/api/workspace
 index: apps/api/src/api/workspace/.pi-map.index.md
 ## role
 Provides REST API endpoints for managing user workspaces, including file operations, Git version control, tool instances, and workspace lifecycle management.
 ## files
 - __init__.py | Aggregates and re-exports workspace-related API routers from submodules for centralized access. | dep: src.api.workspace.workspace_files, src.api.workspace.workspace_git, src.api.workspace.workspace_instances, src.api.workspace.workspaces
 - workspace_files.py | Provides FastAPI endpoints for listing, reading, and writing files within user-owned workspaces with optional Git commit integration. | exp: func:_get_workspace(session: AsyncSession, workspace_id: uuid.UUID, user_id: uuid.UUID) → Workspace, call:session.execute, call:select(Workspace).where, call:result.scalar_one_or_none, raise:HTTPException, func:list_files(workspace_id: uuid.UUID, path, user_id, session) → dict, call:_get_workspace, call:FileService, call:service.list_directory, raise:HTTPException, func:get_file_content(workspace_id: uuid.UUID, path: str, user_id, session) → dict, call:_get_workspace, call:FileService, call:service.read_file, raise:HTTPException, func:write_file(workspace_id: uuid.UUID, data: dict, user_id, session) → dict, call:_get_workspace, call:FileService, call:data.get("path", "").strip, call:data.get("message", "").strip, call:service.write_file, call:GitOperations, call:git.commit, raise:HTTPException | dep: uuid, fastapi, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.services.shared.file_service, sqlalchemy, src.services.git.git_operations
 - workspace_git.py | Provides FastAPI REST endpoints for executing git operations (status, branches, commit, push, pull, fetch, checkout, history) on user workspaces with authentication and database persistence. | exp: func:_get_workspace(session: AsyncSession, workspace_id: uuid.UUID, user_id: uuid.UUID) → Workspace, call:session.execute, call:select(Workspace).where, call:result.scalar_one_or_none, raise:HTTPException, func:git_status(workspace_id: uuid.UUID, user_id, session) → dict, call:_get_workspace, call:GitOperations, call:git.status, raise:HTTPException, func:git_branches(workspace_id: uuid.UUID, user_id, session) → dict, call:_get_workspace, call:GitOperations, call:git.branches, raise:HTTPException, func:git_commit(workspace_id: uuid.UUID, data: dict, user_id, session) → dict, call:_get_workspace, call:data.get("message", "").strip, call:GitOperations, call:git.commit, raise:HTTPException, func:git_push(workspace_id: uuid.UUID, user_id, session) → dict, call:_get_workspace, call:GitOperations, call:git.push, raise:HTTPException, func:git_pull(workspace_id: uuid.UUID, user_id, session) → dict, call:_get_workspace, call:GitOperations, call:git.pull, raise:HTTPException, func:git_fetch(workspace_id: uuid.UUID, user_id, session) → dict, call:_get_workspace, call:GitOperations, call:git.fetch, raise:HTTPException, func:git_checkout(workspace_id: uuid.UUID, data: dict, user_id, session) → dict, call:_get_workspace, call:data.get("branch", "").strip, call:GitOperations, call:git.checkout, call:session.commit, raise:HTTPException, func:git_history(workspace_id: uuid.UUID, path, limit, user_id, session) → dict, call:_get_workspace, call:GitOperations, call:git.history, raise:HTTPException | dep: uuid, fastapi, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.services.git.git_operations, sqlalchemy
 - workspace_instances.py | Defines FastAPI endpoints for creating and listing tool instances associated with a specific workspace. | exp: func:_get_workspace(session: AsyncSession, workspace_id: uuid.UUID, user_id: uuid.UUID) → Workspace, call:session.execute, call:select(Workspace).where, call:result.scalar_one_or_none, raise:HTTPException, func:create_workspace_instance(workspace_id: uuid.UUID, data: CreateWorkspaceInstanceRequest, user_id, session) → dict, call:_get_workspace, call:session.get, call:CreateInstanceRequest, call:str, call:create_tool_instance, call:instance.created_at.isoformat, raise:HTTPException, func:list_workspace_instances(workspace_id: uuid.UUID, user_id, session) → list[dict], call:_get_workspace, call:session.execute, call:select(ToolInstance) .where(ToolInstance.workspace_id == workspace_id) .order_by, call:ToolInstance.created_at.desc, call:result.scalars().all, call:str, call:i.created_at.isoformat | dep: uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, src.auth.dependencies, src.models, src.schemas.tool, src.services.tool.instance_service
 - workspaces.py | FastAPI router providing CRUD endpoints for managing Git workspaces with repository integration, instance tracking, and sync capabilities. | exp: func:list_all_workspaces(user_id, session) → list[dict], call:select(func.count(ToolInstance.id)) .where(ToolInstance.workspace_id == Workspace.id) .correlate(Workspace) .scalar_subquery, call:func.count, call:session.execute, call:select( Workspace, GitRepository, instance_count.label("instance_count"), ) .join(GitRepository, Workspace.repo_id == GitRepository.id) .options(selectinload(GitRepository.project)) .where(Workspace.user_id == user_id) .order_by, call:instance_count.label, call:selectinload, call:Workspace.created_at.desc, call:result.all, call:str, call:ws.last_sync_at.isoformat, call:ws.created_at.isoformat, call:ws.updated_at.isoformat, func:delete_workspace_top_level(workspace_id: uuid.UUID, force, user_id, session) → dict, call:session.get, call:WorkspaceManager, call:manager.delete, call:session.commit, call:session.rollback, call:logger.error, raise:HTTPException, func:create_workspace_top_level(data: dict, user_id, session) → dict, call:data.get("repo_id", "").strip, call:uuid.UUID, call:session.get, call:data.get("name", "").strip, call:data.get("branch", "main").strip, call:WorkspaceManager, call:manager.create, call:session.add, call:session.commit, call:session.rollback, call:logger.error, call:session.refresh, call:str, call:workspace.created_at.isoformat, raise:HTTPException, func:list_workspaces(project_id: uuid.UUID, repo_id: uuid.UUID, user_id, session) → list[dict], call:_get_repo, call:select(func.count(ToolInstance.id)) .where(ToolInstance.workspace_id == Workspace.id) .correlate(Workspace) .scalar_subquery, call:func.count, call:session.execute, call:select( Workspace, instance_count.label("instance_count"), ) .where(Workspace.repo_id == repo_id) .order_by, call:instance_count.label, call:Workspace.created_at.desc, call:result.all, call:str, call:ws.last_sync_at.isoformat, call:ws.created_at.isoformat, call:ws.updated_at.isoformat, func:create_workspace(project_id: uuid.UUID, repo_id: uuid.UUID, data: dict, user_id, session) → dict, call:_get_repo, call:data.get("name", "").strip, call:data.get("branch", "main").strip, call:WorkspaceManager, call:manager.create, call:session.add, call:session.commit, call:session.rollback, call:logger.error, call:session.refresh, call:str, call:workspace.created_at.isoformat, raise:HTTPException, func:get_workspace_detail(project_id: uuid.UUID, repo_id: uuid.UUID, workspace_id: uuid.UUID, user_id, session) → dict, call:_get_repo, call:_get_workspace, call:session.execute, call:select(func.count(ToolInstance.id)).where, call:func.count, call:result.scalar, call:str, call:workspace.last_sync_at.isoformat, call:workspace.created_at.isoformat, call:workspace.updated_at.isoformat, func:update_workspace(project_id: uuid.UUID, repo_id: uuid.UUID, workspace_id: uuid.UUID, data: dict, user_id, session) → dict, call:_get_repo, call:_get_workspace, call:data.get("name", "").strip, call:data.get("branch", "").strip, call:session.commit, call:session.rollback, call:logger.error, call:str, raise:HTTPException, func:delete_workspace(project_id: uuid.UUID, repo_id: uuid.UUID, workspace_id: uuid.UUID, force, user_id, session) → dict, call:_get_repo, call:_get_workspace, call:WorkspaceManager, call:manager.delete, call:session.commit, call:session.rollback, call:logger.error, raise:HTTPException, func:sync_workspace(project_id: uuid.UUID, repo_id: uuid.UUID, workspace_id: uuid.UUID, user_id, session) → dict, call:_get_repo, call:_get_workspace, call:WorkspaceManager, call:manager.sync, call:session.commit, call:workspace.last_sync_at.isoformat, raise:HTTPException, func:_get_repo(session: AsyncSession, repo_id: uuid.UUID, project_id: uuid.UUID, user_id: uuid.UUID) → GitRepository, call:session.execute, call:select(GitRepository) .where( GitRepository.id == repo_id, GitRepository.project_id == project_id, ) .options, call:selectinload, call:result.scalar_one_or_none, raise:HTTPException, func:_get_workspace(session: AsyncSession, workspace_id: uuid.UUID, repo_id: uuid.UUID) → Workspace, call:session.execute, call:select(Workspace).where, call:result.scalar_one_or_none, raise:HTTPException | dep: logging, uuid, fastapi, sqlalchemy, sqlalchemy.ext.asyncio, sqlalchemy.orm, src.auth.dependencies, src.models, src.services.shared.workspace_manager
 ## arch
 Modular FastAPI router decomposition with domain-driven vertical slicing (files/git/instances/workspaces as separate modules), aggregated through __init__.py barrel exports, combining database persistence with external Git repository integration.
 ## tags
 workspace, get, raise:httpexception, call:, at.isoformat, git, call:select, call:data.get
 ## symbols
 - _get_workspace
 - list_files
 - get_file_content
 - write_file
 - git_status
 - git_branches
 - git_commit
 - git_push
 ## workflows
 - change workspace behavior
  read: __init__.py, workspace_files.py, workspace_git.py
 ## dirty
 -
@@ -0,0 +1,17 @@
 """Workspace API routers module."""
 from src.api.workspace.workspace_files import router as workspace_files_router
 from src.api.workspace.workspace_git import router as workspace_git_router
 from src.api.workspace.workspace_instances import router as workspace_instances_router
 from src.api.workspace.workspaces import (
    all_workspaces_router,
    router as workspaces_router,
 )
 __all__ = [
    "all_workspaces_router",
    "workspace_files_router",
    "workspace_git_router",
    "workspace_instances_router",
    "workspaces_router",
 ]
@@ -6,8 +6,8 @@ from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.workspace import Workspace
+from src.models import Workspace
-from src.services.file_service import FileService
+from src.services.shared.file_service import FileService
 router = APIRouter(prefix="/workspaces/{workspace_id}/files")
@@ -103,7 +103,7 @@ async def write_file(
        raise HTTPException(status_code=400, detail=str(exc)) from exc
    if commit_message:
-        from src.services.git_operations import GitOperations
+        from src.services.git.git_operations import GitOperations
        git = GitOperations(workspace)
        try:
@@ -6,8 +6,8 @@ from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.workspace import Workspace
+from src.models import Workspace
-from src.services.git_operations import GitOperations
+from src.services.git.git_operations import GitOperations
 router = APIRouter(prefix="/workspaces/{workspace_id}/git")
@@ -0,0 +1,120 @@
 """Workspace instance API endpoints."""
 import uuid
 from fastapi import APIRouter, Depends, HTTPException, status
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import get_current_user_id, get_db_session
 from src.models import GitRepository
 from src.models import ToolInstance
 from src.models import Workspace
 from src.schemas.tool import CreateInstanceRequest, CreateWorkspaceInstanceRequest
 from src.services.tool.instance_service import create_tool_instance
 router = APIRouter(prefix="/workspaces/{workspace_id}/instances")
 async def _get_workspace(
    session: AsyncSession,
    workspace_id: uuid.UUID,
    user_id: uuid.UUID,
 ) -> Workspace:
    result = await session.execute(
        select(Workspace).where(
            Workspace.id == workspace_id,
            Workspace.user_id == user_id,
        )
    )
    workspace = result.scalar_one_or_none()
    if not workspace:
        raise HTTPException(status_code=404, detail="Workspace not found")
    return workspace
@router.post(
    "/",
    summary="Create instance from workspace",
    description="Create a new tool instance mounted on this workspace.",
    status_code=status.HTTP_201_CREATED,
 )
 async def create_workspace_instance(
    workspace_id: uuid.UUID,
    data: CreateWorkspaceInstanceRequest,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Create a tool instance directly on a workspace."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    repo = await session.get(GitRepository, workspace.repo_id)
    if repo is None:
        raise HTTPException(status_code=404, detail="Repository not found")
    if repo.project_id is None:
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
            detail="Repository is not associated with a project",
        )
    request = CreateInstanceRequest(
        tool_type_id=data.tool_type_id,
        display_name=data.display_name,
        workspace_id=str(workspace.id),
        config_profile_id=data.config_profile_id,
        ssh_key_ids=data.ssh_key_ids,
    )
    try:
        instance = await create_tool_instance(
            session, user_id, repo.project_id, repo.id, request
        )
    except ValueError as exc:
        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
    except RuntimeError as exc:
        raise HTTPException(
            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
        )
    return {
        "id": str(instance.id),
        "name": instance.name,
        "display_name": instance.display_name,
        "tool_type_id": str(instance.tool_type_id),
        "status": instance.status,
        "workspace_id": str(instance.workspace_id) if instance.workspace_id else None,
        "selected_config_profile_id": str(instance.selected_config_profile_id)
        if instance.selected_config_profile_id
        else None,
        "created_at": instance.created_at.isoformat(),
    }
@router.get("/")
 async def list_workspace_instances(
    workspace_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> list[dict]:
    """List tool instances using this workspace."""
    await _get_workspace(session, workspace_id, user_id)
    result = await session.execute(
        select(ToolInstance)
        .where(ToolInstance.workspace_id == workspace_id)
        .order_by(ToolInstance.created_at.desc())
    )
    instances = result.scalars().all()
    return [
        {
            "id": str(i.id),
            "name": i.name,
            "display_name": i.display_name,
            "status": i.status,
            "tool_type_id": str(i.tool_type_id),
            "url": i.url,
            "port": i.port,
            "created_at": i.created_at.isoformat() if i.created_at else None,
        }
        for i in instances
    ]
@@ -9,10 +9,11 @@ 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.models.git_repository import GitRepository
+from src.models import GitRepository
-from src.models.tool_instance import ToolInstance
+from src.models import Project
-from src.models.workspace import Workspace
+from src.models import ToolInstance
-from src.services.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
+from src.models import Workspace
 from src.services.shared.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
 logger = logging.getLogger(__name__)
@@ -36,12 +37,11 @@ async def list_all_workspaces(
    result = await session.execute(
        select(
            Workspace,
-            GitRepository.name.label("repo_name"),
+            GitRepository,
            GitRepository.project_id,
            GitRepository.ssh_key_id.label("repo_ssh_key_id"),
            instance_count.label("instance_count"),
        )
        .join(GitRepository, Workspace.repo_id == GitRepository.id)
        .options(selectinload(GitRepository.project))
        .where(Workspace.user_id == user_id)
        .order_by(Workspace.created_at.desc())
    )
@@ -51,11 +51,11 @@ async def list_all_workspaces(
        {
            "id": str(ws.id),
            "name": ws.name,
-            "repo_id": str(ws.repo_id),
+            "repo_id": str(repo.id),
-            "repo_name": repo_name or "",
+            "repo_name": repo.name or "",
-            "repo_ssh_key_id": str(ssh_key_id) if ssh_key_id else None,
+            "repo_ssh_key_id": str(repo.ssh_key_id) if repo.ssh_key_id else None,
-            "project_id": str(project_id) if project_id else "",
+            "project_id": str(repo.project_id) if repo.project_id else "",
-            "project_name": "",
+            "project_name": repo.project.name if repo.project else "",
            "user_id": str(ws.user_id),
            "branch": ws.branch,
            "path": ws.path,
@@ -65,7 +65,7 @@ async def list_all_workspaces(
            "updated_at": ws.updated_at.isoformat() if ws.updated_at else None,
            "instance_count": count or 0,
        }
-        for ws, repo_name, project_id, ssh_key_id, count in rows
+        for ws, repo, count in rows
    ]
@@ -130,17 +130,26 @@ async def create_workspace_top_level(
    if not name:
        raise HTTPException(status_code=400, detail="Workspace name is required")
    project = await session.get(Project, repo.project_id) if repo.project_id else None
    manager = WorkspaceManager()
    try:
-        workspace = await manager.create(repo, user_id, name, branch, session=session)
+        workspace = await manager.create(
            repo, user_id, name, branch, session=session, project=project
        )
        session.add(workspace)
        await session.commit()
    except HTTPException:
        raise
    except ValueError as exc:
        await session.rollback()
        logger.error("Failed to create workspace: %s", exc)
        raise HTTPException(status_code=400, detail=str(exc)) from exc
    except Exception as exc:
        await session.rollback()
        logger.error("Failed to create workspace: %s", exc)
        raise HTTPException(
-            status_code=409,
+            status_code=500,
-            detail="Workspace name already exists for this repository",
+            detail=f"Failed to create workspace: {exc}",
        ) from exc
    await session.refresh(workspace)
@@ -227,9 +236,12 @@ async def create_workspace(
    if not branch:
        raise HTTPException(status_code=400, detail="Branch is required")
    project = await session.get(Project, project_id)
    manager = WorkspaceManager()
    try:
-        workspace = await manager.create(repo, user_id, name, branch, session=session)
+        workspace = await manager.create(
            repo, user_id, name, branch, session=session, project=project
        )
        session.add(workspace)
        await session.commit()
    except HTTPException:
@@ -242,8 +254,8 @@ async def create_workspace(
        await session.rollback()
        logger.error("Failed to create workspace: %s", exc)
        raise HTTPException(
-            status_code=409,
+            status_code=500,
-            detail="Workspace name already exists for this repository",
+            detail=f"Failed to create workspace: {exc}",
        ) from exc
    await session.refresh(workspace)
@@ -1,60 +0,0 @@
 """Workspace instance API endpoints."""
 import uuid
 from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy import select
 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.workspace import Workspace
 router = APIRouter(prefix="/workspaces/{workspace_id}/instances")
 async def _get_workspace(
    session: AsyncSession,
    workspace_id: uuid.UUID,
    user_id: uuid.UUID,
 ) -> Workspace:
    result = await session.execute(
        select(Workspace).where(
            Workspace.id == workspace_id,
            Workspace.user_id == user_id,
        )
    )
    workspace = result.scalar_one_or_none()
    if not workspace:
        raise HTTPException(status_code=404, detail="Workspace not found")
    return workspace
@router.get("/")
 async def list_workspace_instances(
    workspace_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> list[dict]:
    """List tool instances using this workspace."""
    await _get_workspace(session, workspace_id, user_id)
    result = await session.execute(
        select(ToolInstance)
        .where(ToolInstance.workspace_id == workspace_id)
        .order_by(ToolInstance.created_at.desc())
    )
    instances = result.scalars().all()
    return [
        {
            "id": str(i.id),
            "name": i.name,
            "display_name": i.display_name,
            "status": i.status,
            "tool_type_id": str(i.tool_type_id),
            "url": i.url,
            "port": i.port,
            "created_at": i.created_at.isoformat() if i.created_at else None,
        }
        for i in instances
    ]
@@ -0,0 +1,24 @@
 # apps/api/src/auth (index)
 dir: apps/api/src/auth
 ## role
 Provides authentication and authorization infrastructure for the API, including OIDC login, session management, and dependency injection for protected routes.
 ## parent
 index: apps/api/src/.pi-map.index.md
 map: apps/api/src/.pi-map.md
 ## children
 -
 ## files
 - __init__.py
 - cookies.py
 - dependencies.py
 - oidc.py
 - session.py
 ## links
 index: apps/api/src/auth/.pi-map.index.md
 map: apps/api/src/auth/.pi-map.md
 ## workflows
 - change auth behavior
  read: __init__.py, cookies.py, dependencies.py
 ## dirty
 -
--- a/Show More
+++ b/Show More