fix: constrain dialog content to the viewport

- Add dynamic viewport bounds and scrollable body regions to dialogs and modals\n- Make tool-launch popups use the shared scrollable body pattern\n- Keep mobile sheets, action sheets, and notification popups scroll-contained\n- Restore the ProjectsPage test setup required for the frontend suite\n\nOpenSpec: fix-dialog-scroll-containment\nQuality gates: npm run typecheck, npm run lint, npm test (88 passed), npm run build
Merge fix/terminal-paste-partial-writes into dev
2026-07-15 10:20:20 +00:00 · 2026-07-14 10:34:33 +00:00 · 2026-07-14 10:34:33 +00:00 · 2026-07-14 10:02:30 +00:00 · 2026-07-14 10:02:30 +00:00 · 2026-07-13 13:42:56 +00:00
1301 changed files with 54010 additions and 27386 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/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/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/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/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/alex/projects/headquarter/.claude/skills/sift-backlog/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-archive-change` | Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete. | project | `/home/user/headquarter/.opencode/skills/openspec-archive-change/SKILL.md` |
+| `openspec-explore` | Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change. | project | `/home/user/headquarter/.opencode/skills/openspec-explore/SKILL.md` |
+| `openspec-propose` | Propose a new change with all artifacts generated in one step. Use when the user wants to quickly describe what they want to build and get a complete proposal with design, specs, and tasks ready for implementation. | project | `/home/user/headquarter/.opencode/skills/openspec-propose/SKILL.md` |
+| `sift-backlog` | Triage and organize backlog tasks into actionable plans. Use when asked to review the backlog, prioritize tasks, create plans from backlog items, or move tasks from backlog to open status. Handles the full workflow of listing backlog tasks, grouping related tasks into plans, setting priorities and dependencies, activating plans, and changing task status from backlog to open. | project | `/home/user/headquarter/.claude/skills/sift-backlog/SKILL.md` |

 ## Loading protocol

@@ -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/
@@ -48,8 +49,12 @@ apps/web/dist/
 # OS
 .DS_Store
 Thumbs.db
-
-# Local runtime state
-.atl/
+/.stoneforge/.worktrees/
+# Pi / agent cache
 .pi/
-swap-pane
+.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
+-
@@ -90,13 +90,6 @@ Before completion, report:

 Do not claim completion without verification evidence.

-## Git branch policy
-
- **Default working branch:** `dev` — all commits and pushes target `dev` unless the user explicitly requests otherwise.
- `main` is the stable/production branch; merge to `main` only when explicitly instructed.
- After committing, push to `origin/dev`.
- If `dev` does not exist locally, create it from `main` or fetch it from origin.
-
 ## Git workflow

 ### Branching strategy
@@ -21,7 +21,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **User Settings** - Theme selection, git identity, and preference management
 - **SSH Key Management** - Ed25519 key generation with secure storage
 - **Tool Types** - Built-in development tools (code-server, jupyter-notebook) with custom type support
- **Config Profiles** - User-owned profile CRUD with includes, mounts, path validation, cycle detection, and default profile selection
 - **Comprehensive Documentation** - Architecture, API, deployment, and development guides

 ### Changed
@@ -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
+-
@@ -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 +1,112 @@
+"""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
-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"]
+"""API routers package."""
@@ -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 +1,300 @@
+"""Config profile API endpoints."""
+
+import logging
+import uuid
+
+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.models import ConfigProfile, ConfigProfileInclude, UserConfig
+from src.schemas.config import (
+    ConfigProfileCreate,
+    ConfigProfileIncludeUpdate,
+    ConfigProfileResponse,
+    ConfigProfileUpdate,
+    DefaultProfilesUpdate,
+    ValidateGitUrlRequest,
+    ValidateGitUrlResponse,
+)
+from src.services.config.config_profile_resolver import (
+    ConfigProfileCycleError,
+    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"])
+
+
+@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 [profile_to_response(p) for p in profiles]
+
+
+@router.post(
+    "", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED
+)
+async def create_config_profile(
+    data: ConfigProfileCreate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Create a new config profile."""
+    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 profile_to_response(profile)
+
+
+@router.put("/{profile_id}", response_model=ConfigProfileResponse)
+async def update_config_profile(
+    profile_id: str,
+    data: ConfigProfileUpdate,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Update a config profile."""
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    profile = await update_profile(session, profile, data)
+    logger.debug("Updated config profile %s", profile.id)
+    return profile_to_response(profile)
+
+
+@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_profile(
+    profile_id: str,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Delete a config profile."""
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
+        )
+
+    await session.delete(profile)
+    await session.commit()
+
+    logger.debug("Deleted config profile %s", profile_id)
+    return None
+
+
+@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
+async def update_profile_includes_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)
@@ -1,20 +1,22 @@
 import logging
 import uuid

-from fastapi import APIRouter, Depends, HTTPException, status
+from fastapi import APIRouter, Depends
 from sqlalchemy import select
 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.schemas.user_config import UserConfigResponse, UserConfigUpdate
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
+from src.models import UserConfig
+from src.schemas.user import UserConfigResponse, UserConfigUpdate
+
+logger = logging.getLogger(__name__)

 router = APIRouter(prefix="/users/me", tags=["user-config"])


-
-async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> UserConfig:
+async def _get_or_create_config(
+    session: AsyncSession, user_id: uuid.UUID
+) -> UserConfig:
    """Get or create user config record.

    Args:
@@ -24,10 +26,12 @@ async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> Us
    Returns:
        The user's config, creating a new one if it doesn't exist.
    """
-    result = await session.execute(select(UserConfig).where(UserConfig.user_id == user.id))
+    result = await session.execute(
+        select(UserConfig).where(UserConfig.user_id == user_id)
+    )
    config = result.scalar_one_or_none()
    if config is None:
-        config = UserConfig(user_id=user.id, config={})
+        config = UserConfig(user_id=user_id, config={})
        session.add(config)
        await session.commit()
        await session.refresh(config)
@@ -41,7 +45,7 @@ async def _get_or_create_config(session: AsyncSession, user_id: uuid.UUID) -> Us
    description="Get the current user's configuration settings.",
 )
 async def get_user_config(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
    """Get the current user's configuration.
@@ -53,7 +57,8 @@ async def get_user_config(
    Returns:
        The user's configuration settings.
    """
-    config = await _get_or_create_config(session, user.id)
+    _user = await _get_user(session, user_id)
+    config = await _get_or_create_config(session, user_id)
    return UserConfigResponse.model_validate(config.config)


@@ -65,7 +70,7 @@ async def get_user_config(
 )
 async def update_user_config(
    data: UserConfigUpdate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> UserConfigResponse:
    """Update the current user's configuration.
@@ -78,15 +83,16 @@ async def update_user_config(
    Returns:
        The updated user configuration.
    """
-    config = await _get_or_create_config(session, user.id)
+    _user = await _get_user(session, user_id)
+    config = await _get_or_create_config(session, user_id)

    # Merge updates
    update_data = data.model_dump(exclude_unset=True)
-    logger.info("Updating user config for user %s: %s", user.id, update_data)
+    logger.debug("Updating user config for user %s: %s", user_id, update_data)
    # SQLAlchemy JSON doesn't track dict mutations, so we replace the whole dict
    config.config = {**config.config, **update_data}

    await session.commit()
    await session.refresh(config)
-    logger.info("Updated config: %s", config.config)
+    logger.debug("Updated config: %s", config.config)
    return UserConfigResponse.model_validate(config.config)
@@ -1,299 +0,0 @@
-"""Config profile API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, 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.models.config_include import ConfigInclude
-from src.models.config_mount import ConfigMount
-from src.models.config_profile import ConfigProfile
-from src.models.tool_type import ToolType
-from src.models.user_config import UserConfig
-from src.schemas.config_profile import (
-    ConfigIncludeCreate,
-    ConfigIncludeUpdate,
-    ConfigMountCreate,
-    ConfigMountUpdate,
-    ConfigProfileCreate,
-    ConfigProfileUpdate,
-    DefaultProfilesUpdate,
-)
-from src.services.config_profiles import (
-    check_duplicate_include,
-    check_duplicate_mount_path,
-    check_duplicate_name,
-    get_default_profile_for_tool_type,
-    get_default_profiles,
-    get_owned_profile,
-    include_to_dict,
-    list_includes_for_profile,
-    list_mounts_for_profile,
-    mount_to_dict,
-    profile_to_dict,
-    set_default_profiles,
-    validate_includes_no_cycle,
-)
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
-
-
-
-@router.get("")
-async def list_config_profiles(
-    tool_type_id: str | None = None,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    query = select(ConfigProfile).where(ConfigProfile.user_id == user_id)
-    if tool_type_id:
-        tool_type = await session.get(ToolType, uuid.UUID(tool_type_id))
-        if tool_type is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-    result = await session.execute(query.order_by(ConfigProfile.name))
-    return {"profiles": [profile_to_dict(p) for p in result.scalars().all()]}
-
-
-@router.post("", status_code=status.HTTP_201_CREATED)
-async def create_config_profile(
-    data: ConfigProfileCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await check_duplicate_name(session, user_id, data.name)
-    profile = ConfigProfile(user_id=user_id, name=data.name, description=data.description)
-    session.add(profile)
-    await session.commit()
-    await session.refresh(profile)
-    return profile_to_dict(profile)
-
-
-@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:
-    return await get_default_profiles(session, user_id)
-
-
-@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:
-    return await set_default_profiles(session, user_id, data.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:
-    return await get_default_profile_for_tool_type(session, user_id, tool_type_id)
-
-
-@router.get("/{profile_id}")
-async def get_config_profile(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    profile = await session.get(
-        ConfigProfile,
-        profile_id,
-        options=[selectinload(ConfigProfile.includes), selectinload(ConfigProfile.mounts)],
-    )
-    if profile is None or profile.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config profile not found")
-    includes_data = []
-    for inc in profile.includes:
-        included_profile = await session.get(ConfigProfile, inc.included_profile_id)
-        includes_data.append(include_to_dict(inc, included_profile.name if included_profile else None))
-    return {
-        **profile_to_dict(profile),
-        "includes": includes_data,
-        "mounts": [mount_to_dict(m) for m in profile.mounts],
-    }
-
-
-@router.put("/{profile_id}")
-async def update_config_profile(
-    profile_id: uuid.UUID,
-    data: ConfigProfileUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    profile = await get_owned_profile(profile_id, user_id, session)
-    if data.name is not None:
-        await check_duplicate_name(session, user_id, data.name, exclude_id=profile_id)
-        profile.name = data.name
-    if data.description is not None:
-        profile.description = data.description
-    await session.commit()
-    await session.refresh(profile)
-    return profile_to_dict(profile)
-
-
-@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_config_profile(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    profile = await get_owned_profile(profile_id, user_id, session)
-    await session.delete(profile)
-    await session.commit()
-
-
-
-@router.get("/{profile_id}/includes")
-async def list_profile_includes(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await get_owned_profile(profile_id, user_id, session)
-    return await list_includes_for_profile(session, profile_id)
-
-
-@router.post("/{profile_id}/includes", status_code=status.HTTP_201_CREATED)
-async def add_profile_include(
-    profile_id: uuid.UUID,
-    data: ConfigIncludeCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    profile = await get_owned_profile(profile_id, user_id, session)
-    included_profile_id = uuid.UUID(data.included_profile_id)
-    if included_profile_id == profile_id:
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="a profile cannot include itself")
-    included_profile = await session.get(ConfigProfile, included_profile_id)
-    if included_profile is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="included profile not found")
-    if included_profile.user_id != user_id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="included profile does not belong to user")
-    await check_duplicate_include(session, profile_id, included_profile_id)
-    await validate_includes_no_cycle(session, profile_id, included_profile_id)
-    include = ConfigInclude(
-        profile_id=profile_id,
-        included_profile_id=included_profile_id,
-        order_index=data.order_index,
-    )
-    session.add(include)
-    await session.commit()
-    await session.refresh(include)
-    return include_to_dict(include, included_profile.name)
-
-
-@router.put("/{profile_id}/includes/{include_id}")
-async def update_profile_include(
-    profile_id: uuid.UUID,
-    include_id: uuid.UUID,
-    data: ConfigIncludeUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await get_owned_profile(profile_id, user_id, session)
-    include = await session.get(ConfigInclude, include_id)
-    if include is None or include.profile_id != profile_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="include not found")
-    include.order_index = data.order_index
-    await session.commit()
-    await session.refresh(include)
-    included_profile = await session.get(ConfigProfile, include.included_profile_id)
-    return include_to_dict(include, included_profile.name if included_profile else None)
-
-
-@router.delete("/{profile_id}/includes/{include_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def remove_profile_include(
-    profile_id: uuid.UUID,
-    include_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    await get_owned_profile(profile_id, user_id, session)
-    include = await session.get(ConfigInclude, include_id)
-    if include is None or include.profile_id != profile_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="include not found")
-    await session.delete(include)
-    await session.commit()
-
-
-
-@router.get("/{profile_id}/mounts")
-async def list_profile_mounts(
-    profile_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await get_owned_profile(profile_id, user_id, session)
-    return await list_mounts_for_profile(session, profile_id)
-
-
-@router.post("/{profile_id}/mounts", status_code=status.HTTP_201_CREATED)
-async def add_profile_mount(
-    profile_id: uuid.UUID,
-    data: ConfigMountCreate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    profile = await get_owned_profile(profile_id, user_id, session)
-    await check_duplicate_mount_path(session, profile_id, data.target_path)
-    mount = ConfigMount(
-        profile_id=profile_id,
-        target_path=data.target_path,
-        mode=data.mode,
-        files=data.files,
-        order_index=data.order_index,
-    )
-    session.add(mount)
-    await session.commit()
-    await session.refresh(mount)
-    return mount_to_dict(mount)
-
-
-@router.put("/{profile_id}/mounts/{mount_id}")
-async def update_profile_mount(
-    profile_id: uuid.UUID,
-    mount_id: uuid.UUID,
-    data: ConfigMountUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    await get_owned_profile(profile_id, user_id, session)
-    mount = await session.get(ConfigMount, mount_id)
-    if mount is None or mount.profile_id != profile_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="mount not found")
-    if data.target_path is not None:
-        await check_duplicate_mount_path(session, profile_id, data.target_path, exclude_id=mount_id)
-        mount.target_path = data.target_path
-    if data.files is not None:
-        mount.files = data.files
-    if data.order_index is not None:
-        mount.order_index = data.order_index
-    await session.commit()
-    await session.refresh(mount)
-    return mount_to_dict(mount)
-
-
-@router.delete("/{profile_id}/mounts/{mount_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def remove_profile_mount(
-    profile_id: uuid.UUID,
-    mount_id: uuid.UUID,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    await get_owned_profile(profile_id, user_id, session)
-    mount = await session.get(ConfigMount, mount_id)
-    if mount is None or mount.profile_id != profile_id:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="mount not found")
-    await session.delete(mount)
-    await session.commit()
@@ -1,290 +0,0 @@
-"""Git repository API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, Response, status
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user, get_db_session, get_owned_project
-from src.models.project import Project
-from src.models.user import User
-from src.schemas.git_repository import (
-    BranchCreateRequest,
-    CheckoutRequest,
-    CommitRequest,
-    CommitResponse,
-    FetchResponse,
-    FileContentResponse,
-    FileListResponse,
-    FileUpdateRequest,
-    FileUpdateResponse,
-    GitRepositoryCreate,
-    GitRepositoryResponse,
-    MergeRequest,
-    MergeResponse,
-    PullResponse,
-    PushResponse,
-    StatusResponse,
-    URLParseRequest,
-    URLParseResponse,
-)
-from src.services.git import control as git_control
-from src.services.git import files as git_files
-from src.services.git.repository import create_repository, delete_repository, list_repositories
-from src.utils.git_url_parser import parse_git_url
-
-router = APIRouter(prefix="/projects", tags=["git-repositories"])
-logger = logging.getLogger(__name__)
-
-
-@router.get("/{project_id}/repositories", response_model=list[GitRepositoryResponse])
-async def list_repositories_endpoint(
-    project_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-):
-    return await list_repositories(session, project_id)
-
-
-@router.post("/{project_id}/repositories", response_model=GitRepositoryResponse, status_code=status.HTTP_201_CREATED)
-async def create_repository_endpoint(
-    project_id: uuid.UUID,
-    data: GitRepositoryCreate,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-):
-    return await create_repository(session, project_id, data, user)
-
-
-@router.delete("/{project_id}/repositories/{repo_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_repository_endpoint(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-):
-    await delete_repository(session, repo_id, project_id)
-    return Response(status_code=status.HTTP_204_NO_CONTENT)
-
-
-@router.post("/repositories/parse-url", response_model=URLParseResponse)
-async def parse_repository_url(data: URLParseRequest) -> URLParseResponse:
-    return URLParseResponse(**parse_git_url(data.url))
-
-
-# History
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    from src.utils.git_history import get_commit_history
-    from src.services.git.repository import get_repo_and_validate, ensure_repo_on_disk
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        return get_commit_history(repo.path, branch=branch, limit=limit, offset=offset)
-    except RuntimeError as e:
-        logger.warning("Git history failed for %s: %s", repo.path, str(e))
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"Git history unavailable: {str(e)}",
-        ) from 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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    from src.utils.git_history import get_commit_detail
-    from src.services.git.repository import get_repo_and_validate, ensure_repo_on_disk
-    repo = await get_repo_and_validate(session, repo_id, project_id)
-    ensure_repo_on_disk(repo)
-    try:
-        return get_commit_detail(repo.path, commit_hash)
-    except RuntimeError as e:
-        logger.warning("Git commit detail failed for %s %s: %s", repo.path, commit_hash, str(e))
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"Commit detail unavailable: {str(e)}",
-        ) from e
-
-
-# File browsing
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileListResponse:
-    return await git_files.list_files(session, project_id, repo_id, branch, path)
-
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileContentResponse:
-    return await git_files.get_file(session, project_id, repo_id, branch, path)
-
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> FileUpdateResponse:
-    return await git_files.update_file(session, project_id, repo_id, data, user)
-
-
-# Branches
-
-@router.get("/{project_id}/repositories/{repo_id}/branches")
-async def get_repository_branches(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    return await git_files.list_branches_with_validation(session, project_id, repo_id)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/branches")
-async def create_repository_branch(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: BranchCreateRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    return await git_control.create_branch_with_validation(session, project_id, repo_id, data)
-
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    return await git_control.delete_branch_with_validation(session, project_id, repo_id, branch_name, force)
-
-
-@router.post("/{project_id}/repositories/{repo_id}/checkout")
-async def checkout_repository_branch(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CheckoutRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    return await git_control.checkout_branch_with_validation(session, project_id, repo_id, data)
-
-
-# Git control
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> StatusResponse:
-    return await git_control.get_status_with_validation(session, project_id, repo_id)
-
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> CommitResponse:
-    result = await git_control.commit_changes_with_validation(session, project_id, repo_id, data, user)
-    return CommitResponse(commit_hash=result["commit_hash"], message=result["message"])
-
-
-@router.post("/{project_id}/repositories/{repo_id}/fetch", response_model=FetchResponse)
-async def fetch_repository(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> FetchResponse:
-    return await git_control.fetch_with_validation(session, project_id, repo_id)
-
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> PullResponse:
-    return await git_control.pull_with_validation(session, project_id, repo_id, branch)
-
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> PushResponse:
-    return await git_control.push_with_validation(session, project_id, repo_id, branch)
-
-
-@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: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> MergeResponse:
-    return await git_control.merge_with_validation(session, project_id, repo_id, data)
@@ -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))
@@ -3,25 +3,29 @@ import shutil
 import uuid

 from fastapi import APIRouter, Depends, HTTPException, Response, status
-from sqlalchemy import select
+from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession

-from src.auth.dependencies import get_current_user, get_db_session, get_owned_project
-from src.models.git_repository import GitRepository
+from src.auth.dependencies import (
+    _get_owned_project,
+    _get_user,
+    get_current_user_id,
+    get_db_session,
+)
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
-from src.models.user import User
+from src.models import SSHKey
+from src.models import ToolInstance
 from src.schemas.project import (
    ProjectCreate,
-    ProjectUpdate,
    ProjectResponse,
+    ProjectUpdate,
    SetDefaultSSHKeyRequest,
 )

 router = APIRouter(prefix="/projects", tags=["projects"])


-
@router.post(
    "",
    response_model=ProjectResponse,
@@ -31,7 +35,7 @@ router = APIRouter(prefix="/projects", tags=["projects"])
 )
 async def create_project(
    data: ProjectCreate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> Project:
    """Create a new project.
@@ -44,6 +48,7 @@ async def create_project(
    Returns:
        The newly created project.
    """
+    user = await _get_user(session, user_id)
    project = Project(
        name=data.name,
        description=data.description,
@@ -58,25 +63,77 @@ async def create_project(

@router.get(
    "",
-    response_model=list[ProjectResponse],
    summary="List all projects",
-    description="Retrieve all projects owned by the authenticated user.",
+    description="Retrieve all projects owned by the authenticated user with repositories and workspaces.",
 )
 async def list_projects(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
-) -> list[Project]:
+) -> list[dict]:
    """List all projects for the authenticated user.

-    Args:
-        user_id: ID of the authenticated user.
-        session: Database session.
-
-    Returns:
-        List of projects owned by the user.
+    Returns projects with nested repositories and workspaces for inline display.
    """
-    result = await session.execute(select(Project).where(Project.owner_id == user.id))
-    return list(result.scalars().all())
+    user = await _get_user(session, user_id)
+    result = await session.execute(
+        select(Project)
+        .where(Project.owner_id == user.id)
+        .order_by(Project.created_at.desc())
+    )
+    projects = result.scalars().all()
+
+    from src.models import Workspace
+
+    enriched = []
+    for project in projects:
+        repos_result = await session.execute(
+            select(GitRepository).where(GitRepository.project_id == project.id)
+        )
+        repositories = []
+        for repo in repos_result.scalars().all():
+            ws_result = await session.execute(
+                select(Workspace).where(Workspace.repo_id == repo.id)
+            )
+            workspaces = []
+            for ws in ws_result.scalars().all():
+                # Count instances
+                inst_result = await session.execute(
+                    select(func.count()).where(ToolInstance.workspace_id == ws.id)
+                )
+                instance_count = inst_result.scalar() or 0
+                workspaces.append(
+                    {
+                        "id": str(ws.id),
+                        "name": ws.name,
+                        "branch": ws.branch,
+                        "status": ws.status,
+                        "instance_count": instance_count,
+                    }
+                )
+
+            repositories.append(
+                {
+                    "id": str(repo.id),
+                    "name": repo.name,
+                    "remote_url": repo.remote_url,
+                    "workspaces": workspaces,
+                }
+            )
+
+        enriched.append(
+            {
+                "id": str(project.id),
+                "name": project.name,
+                "description": project.description,
+                "owner_id": str(project.owner_id),
+                "repositories": repositories,
+                "created_at": project.created_at.isoformat()
+                if project.created_at
+                else None,
+            }
+        )
+
+    return enriched


@router.get(
@@ -87,8 +144,7 @@ async def list_projects(
 )
 async def get_project(
    project_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> Project:
    """Get a specific project by ID.
@@ -101,8 +157,8 @@ async def get_project(
    Returns:
        The requested project.
    """
-    return project
-
+    await _get_user(session, user_id)
+    return await _get_owned_project(project_id, user_id, session)


@router.patch(
@@ -114,8 +170,7 @@ async def get_project(
 async def update_project(
    project_id: uuid.UUID,
    data: ProjectUpdate,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> Project:
    """Update a project.
@@ -129,6 +184,8 @@ async def update_project(
    Returns:
        The updated project.
    """
+    await _get_user(session, user_id)
+    project = await _get_owned_project(project_id, user_id, session)

    if data.name is not None:
        project.name = data.name
@@ -148,8 +205,7 @@ async def update_project(
 )
 async def delete_project(
    project_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> Response:
    """Delete a project and all its repositories.
@@ -162,9 +218,13 @@ async def delete_project(
    Returns:
        Empty response with 204 status code.
    """
+    await _get_user(session, user_id)
+    project = await _get_owned_project(project_id, user_id, session)

    # Delete repositories from disk and database
-    result = await session.execute(select(GitRepository).where(GitRepository.project_id == project_id))
+    result = await session.execute(
+        select(GitRepository).where(GitRepository.project_id == project_id)
+    )
    repositories = result.scalars().all()
    for repo in repositories:
        if os.path.exists(repo.path):
@@ -185,8 +245,7 @@ async def delete_project(
 async def set_default_ssh_key(
    project_id: uuid.UUID,
    data: SetDefaultSSHKeyRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> Project:
    """Set the default SSH key for a project.
@@ -200,6 +259,8 @@ async def set_default_ssh_key(
    Returns:
        The updated project.
    """
+    user = await _get_user(session, user_id)
+    project = await _get_owned_project(project_id, user_id, session)

    ssh_key = await session.get(SSHKey, data.ssh_key_id)
    if ssh_key is None or ssh_key.user_id != user.id:
@@ -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"])

@@ -4,12 +4,11 @@ import time
 from datetime import datetime, timezone
 from typing import Any

-from fastapi import APIRouter, status
+from fastapi import APIRouter
 from sqlalchemy import text

-from src.config import Settings
 from src.database import SessionLocal
-from src.schemas.health import (
+from src.schemas.system import (
    DatabaseHealth,
    DatabaseHealthResponse,
    DiskHealth,
@@ -8,8 +8,8 @@ from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
 from sqlalchemy.ext.asyncio import AsyncSession

 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import ToolInstance
+from src.models import ToolType

 logger = logging.getLogger(__name__)

@@ -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.services.notification_service import notification_service
+from src.models import UserConfig
+from src.services.shared.notification_service import notification_service

 router = APIRouter(prefix="/notifications", tags=["notifications"])

@@ -12,10 +12,21 @@ 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.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.services.terminal_manager import MaxSessionsExceededError, terminal_manager
+from src.models import (
+    TerminalSessionModel,
+    ToolDefinitionManifest,
+    ToolInstance,
+    ToolType,
+)
+from src.services.build.manifest_compiler import (
+    deep_merge,
+    get_manifest_container_user,
+    resolve_base,
+)
+from src.services.terminal.terminal_manager import (
+    MaxSessionsExceededError,
+    terminal_manager,
+)

 router = APIRouter()
 logger = logging.getLogger(__name__)
@@ -57,6 +68,39 @@ 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 +183,7 @@ 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 +193,14 @@ 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 +211,7 @@ 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 +242,7 @@ 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(
@@ -280,65 +334,73 @@ async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> N
                    await session.write_input(message["bytes"])
                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)
-                            msg_type = ctrl.get("type")
-
-                            if msg_type == "resize":
-                                cols = ctrl.get("cols", 80)
-                                rows = ctrl.get("rows", 24)
-                                logger.debug(
-                                    "Received resize message for instance %s: %sx%s",
-                                    instance_id,
-                                    cols,
-                                    rows,
-                                )
-                                await session.resize(cols, rows)
-                            elif msg_type == "ack":
-                                char_count = ctrl.get("chars", 0)
-                                if char_count > 0:
-                                    session.acknowledge_data(char_count)
-                            elif msg_type == "reset":
-                                # Reset terminal session (scoped to current slot)
-                                logger.debug(
-                                    "Resetting terminal session for instance %s (slot=%s)",
-                                    session.instance_id,
-                                    session_ref.slot_session_id,
-                                )
-                                await websocket.send_json(
-                                    {"type": "status", "status": "resetting"}
-                                )
-
-                                # Reset the session scoped to its slot
-                                new_session = await terminal_manager.reset_session(
-                                    session.instance_id,
-                                    session.container_id,
-                                    startup_command=session.startup_command,
-                                    session_id=session_ref.slot_session_id,
-                                    name=session.name,
-                                )
-
-                                # Update the mutable session reference
-                                session_ref.session = new_session
-
-                                # Attach to new session
-                                await terminal_manager.attach_websocket(
-                                    new_session, websocket
-                                )
-                                await websocket.send_json(
-                                    {"type": "status", "status": "connected"}
-                                )
-
-                                # Continue the loop with the new session
-                                continue
-
+                            parsed = json.loads(text)
                        except json.JSONDecodeError:
-                            # Not a valid JSON control message, treat as regular input
-                            await session.write_input(text.encode("utf-8"))
-                    else:
+                            parsed = None
+                        if isinstance(parsed, dict) and "type" in parsed:
+                            ctrl = parsed
+
+                    if ctrl is None:
                        await session.write_input(text.encode("utf-8"))
+                        continue
+
+                    msg_type = ctrl["type"]
+                    if msg_type == "resize":
+                        cols = ctrl.get("cols", 80)
+                        rows = ctrl.get("rows", 24)
+                        logger.debug(
+                            "Received resize message for instance %s: %sx%s",
+                            instance_id,
+                            cols,
+                            rows,
+                        )
+                        await session.resize(cols, rows)
+                    elif msg_type == "ack":
+                        char_count = ctrl.get("chars", 0)
+                        if char_count > 0:
+                            session.acknowledge_data(char_count)
+                    elif msg_type == "reset":
+                        # Reset terminal session (scoped to current slot)
+                        logger.debug(
+                            "Resetting terminal session for instance %s (slot=%s)",
+                            session.instance_id,
+                            session_ref.slot_session_id,
+                        )
+                        await websocket.send_json(
+                            {"type": "status", "status": "resetting"}
+                        )
+
+                        # Reset the session scoped to its slot
+                        new_session = await terminal_manager.reset_session(
+                            session.instance_id,
+                            session.container_id,
+                            startup_command=session.startup_command,
+                            session_id=session_ref.slot_session_id,
+                            name=session.name,
+                            container_user=session.container_user,
+                        )
+
+                        # Update the mutable session reference
+                        session_ref.session = new_session
+
+                        # Attach to new session
+                        await terminal_manager.attach_websocket(new_session, websocket)
+                        await websocket.send_json(
+                            {"type": "status", "status": "connected"}
+                        )
+
+                        # Continue the loop with the new session
+                        continue
            elif message["type"] == "websocket.disconnect":
                break
    except Exception:
@@ -486,6 +548,7 @@ 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 +556,7 @@ async def create_terminal_session(
            instance.container_id,
            startup_command=startup_command,
            name=name,
+            container_user=container_user,
        )
    except MaxSessionsExceededError:
        raise HTTPException(
@@ -595,6 +659,7 @@ 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 +667,7 @@ async def reset_specific_terminal_session(
        startup_command=startup_command,
        session_id=key[1],
        name=name,
+        container_user=container_user,
    )

    return {
@@ -687,6 +753,7 @@ 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 +761,7 @@ 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.tool_type import ToolType
-from src.services.manifest_compiler import (
+from src.models import ToolDefinitionManifest
+from src.models import ToolType
+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
+        )
@@ -1,14 +1,18 @@
 import uuid

-import yaml
 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, get_db_session
-from src.models.tool_type import ToolType
+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 import ToolType
 from src.models.user import User
-from src.schemas.tool_type import (
+from src.schemas.tool import (
    ToolTypeCreate,
    ToolTypeResponse,
    ToolTypeUpdate,
@@ -38,7 +42,7 @@ async def _require_admin(user: User) -> None:
 )
 async def create_tool_type(
    data: ToolTypeCreate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
    """Create a new tool type.
@@ -51,6 +55,7 @@ async def create_tool_type(
    Returns:
        The newly created tool type.
    """
+    user = await _get_user(session, user_id)
    await _require_admin(user)

    # Check for duplicate name
@@ -67,13 +72,16 @@ async def create_tool_type(
        description=data.description,
        default_port=data.default_port,
        definition_type=data.definition_type,
+        manifest_id=data.manifest_id,
        compose_template=data.compose_template,
        dockerfile_template=data.dockerfile_template,
        build_context=data.build_context,
        readiness_probe=data.readiness_probe,
+        startup_command=data.startup_command,
        required_variables=data.required_variables,
        category=data.category,
-        interfaces=data.interfaces,
+        interface_type=data.interface_type,
+        requires_port=data.requires_port,
        created_by_id=user.id,
    )
    session.add(tool_type)
@@ -89,7 +97,7 @@ async def create_tool_type(
    description="List all available tool types including built-in and custom ones.",
 )
 async def list_tool_types(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> list[ToolType]:
    """List all tool types.
@@ -101,6 +109,7 @@ async def list_tool_types(
    Returns:
        List of all tool types ordered by name.
    """
+    await _get_user(session, user_id)
    result = await session.execute(select(ToolType).order_by(ToolType.name))
    return list(result.scalars().all())

@@ -113,7 +122,7 @@ async def list_tool_types(
 )
 async def get_tool_type(
    tool_type_id: uuid.UUID,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
    """Get a specific tool type by ID.
@@ -126,6 +135,7 @@ async def get_tool_type(
    Returns:
        The requested tool type.
    """
+    await _get_user(session, user_id)
    tool_type = await session.get(ToolType, tool_type_id)
    if tool_type is None:
        raise HTTPException(
@@ -143,7 +153,7 @@ async def get_tool_type(
 async def update_tool_type(
    tool_type_id: uuid.UUID,
    data: ToolTypeUpdate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> ToolType:
    """Update a tool type.
@@ -157,6 +167,7 @@ async def update_tool_type(
    Returns:
        The updated tool type.
    """
+    user = await _get_user(session, user_id)
    await _require_admin(user)

    tool_type = await session.get(ToolType, tool_type_id)
@@ -165,16 +176,13 @@ async def update_tool_type(
            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
        )

-    if tool_type.is_builtin:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN,
-            detail="cannot modify built-in tool types",
-        )
+    # Built-in tool types can now be modified

    update_data = data.model_dump(exclude_unset=True)

    # Validate port if being updated
-    if "default_port" in update_data:
+    requires_port = update_data.get("requires_port", tool_type.requires_port)
+    if "default_port" in update_data and requires_port:
        new_port = update_data["default_port"]
        if new_port <= 0 or new_port > 65535:
            raise HTTPException(
@@ -188,62 +196,35 @@ async def update_tool_type(
            template = update_data.get("compose_template", tool_type.compose_template)
            if template:
                try:
-                    parsed = yaml.safe_load(template)
-                except yaml.YAMLError:
-                    parsed = None
-
-                if parsed and isinstance(parsed, dict) and "services" in parsed:
-                    port_str = str(new_port)
-                    port_exposed = False
-                    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
-                                ):
-                                    port_exposed = True
-                                    break
-                                elif (
-                                    isinstance(port_mapping, int)
-                                    and port_mapping == new_port
-                                ):
-                                    port_exposed = True
-                                    break
-                        if port_exposed:
-                            break
-
-                    if not port_exposed:
+                    parsed = validate_compose_yaml(template)
+                    if not check_port_exposed(parsed, new_port):
                        raise HTTPException(
                            status_code=status.HTTP_400_BAD_REQUEST,
                            detail=f"Port {new_port} is not exposed in the compose template",
                        )
+                except ValueError as e:
+                    raise HTTPException(
+                        status_code=status.HTTP_400_BAD_REQUEST, detail=str(e)
+                    )

    # Validate required variables for compose definitions
    definition_type = update_data.get("definition_type", tool_type.definition_type)
    if definition_type == "compose":
        if "required_variables" in update_data and "compose_template" in update_data:
-            template = update_data["compose_template"]
-            for var in update_data["required_variables"]:
-                placeholder = f"{{{{{var}}}}}"
-                if placeholder not in template:
-                    raise HTTPException(
-                        status_code=status.HTTP_400_BAD_REQUEST,
-                        detail=f"Required variable '{var}' not found in compose template",
-                    )
+            validate_required_variables(
+                update_data["compose_template"], update_data["required_variables"]
+            )
        elif "required_variables" in update_data:
            template = tool_type.compose_template
            if template:
-                for var in update_data["required_variables"]:
-                    placeholder = f"{{{{{var}}}}}"
-                    if placeholder not in template:
-                        raise HTTPException(
-                            status_code=status.HTTP_400_BAD_REQUEST,
-                            detail=f"Required variable '{var}' not found in compose template",
-                        )
+                validate_required_variables(template, update_data["required_variables"])
+
+    # When switching to manifest, clear legacy templates
+    if definition_type == "manifest":
+        if "manifest_id" in update_data:
+            tool_type.manifest_id = update_data["manifest_id"]
+        tool_type.compose_template = None
+        tool_type.dockerfile_template = None

    for field, value in update_data.items():
        setattr(tool_type, field, value)
@@ -260,7 +241,7 @@ async def update_tool_type(
 )
 async def validate_tool_type_template(
    data: ToolTypeValidateRequest,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Validate a tool type template syntax.
@@ -273,6 +254,7 @@ async def validate_tool_type_template(
    Returns:
        Validation result with success status and any errors.
    """
+    await _get_user(session, user_id)

    errors = []

@@ -281,15 +263,9 @@ async def validate_tool_type_template(
            errors.append("Compose template is required")
        else:
            try:
-                parsed = yaml.safe_load(data.compose_template)
-                if not isinstance(parsed, dict):
-                    errors.append("Compose template must be a YAML mapping")
-                elif "services" not in parsed:
-                    errors.append("Compose template must contain 'services' key")
-                elif not parsed["services"]:
-                    errors.append("Compose template must define at least one service")
-            except yaml.YAMLError as e:
-                errors.append(f"Invalid YAML: {e}")
+                validate_compose_yaml(data.compose_template)
+            except ValueError as e:
+                errors.append(str(e))

    elif data.definition_type == "dockerfile":
        if not data.dockerfile_template:
@@ -297,8 +273,11 @@ async def validate_tool_type_template(
        elif not data.dockerfile_template.strip().startswith("FROM"):
            errors.append("Dockerfile must start with a FROM instruction")

+    elif data.definition_type == "manifest":
+        pass  # Manifest validation is handled separately
+
    else:
-        errors.append("definition_type must be 'compose' or 'dockerfile'")
+        errors.append("definition_type must be 'compose', 'dockerfile', or 'manifest'")

    return {
        "valid": len(errors) == 0,
@@ -313,7 +292,7 @@ async def validate_tool_type_template(
 )
 async def validate_tool_type(
    tool_type_id: uuid.UUID,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Validate a tool type's template syntax.
@@ -326,6 +305,7 @@ async def validate_tool_type(
    Returns:
        Validation result with success status and any errors.
    """
+    await _get_user(session, user_id)
    tool_type = await session.get(ToolType, tool_type_id)
    if tool_type is None:
        raise HTTPException(
@@ -339,15 +319,9 @@ async def validate_tool_type(
            errors.append("Compose template is empty")
        else:
            try:
-                parsed = yaml.safe_load(tool_type.compose_template)
-                if not isinstance(parsed, dict):
-                    errors.append("Compose template must be a YAML mapping")
-                elif "services" not in parsed:
-                    errors.append("Compose template must contain 'services' key")
-                elif not parsed["services"]:
-                    errors.append("Compose template must define at least one service")
-            except yaml.YAMLError as e:
-                errors.append(f"Invalid YAML: {e}")
+                validate_compose_yaml(tool_type.compose_template)
+            except ValueError as e:
+                errors.append(str(e))

    elif tool_type.definition_type == "dockerfile":
        if not tool_type.dockerfile_template:
@@ -355,6 +329,10 @@ async def validate_tool_type(
        elif not tool_type.dockerfile_template.strip().startswith("FROM"):
            errors.append("Dockerfile must start with a FROM instruction")

+    elif tool_type.definition_type == "manifest":
+        if not tool_type.manifest_id:
+            errors.append("Manifest reference is missing")
+
    return {
        "valid": len(errors) == 0,
        "errors": errors,
@@ -369,7 +347,7 @@ async def validate_tool_type(
 )
 async def delete_tool_type(
    tool_type_id: uuid.UUID,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> None:
    """Delete a tool type.
@@ -382,6 +360,7 @@ async def delete_tool_type(
    Returns:
        None with 204 status code.
    """
+    user = await _get_user(session, user_id)
    await _require_admin(user)

    tool_type = await session.get(ToolType, tool_type_id)
@@ -390,11 +369,7 @@ async def delete_tool_type(
            status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found"
        )

-    if tool_type.is_builtin:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN,
-            detail="cannot delete built-in tool types",
-        )
+    # Built-in tool types can now be deleted

    await session.delete(tool_type)
    await session.commit()
@@ -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:
-                    return True
+                if isinstance(port_mapping, str):
+                    # 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

@@ -1,286 +0,0 @@
-"""Tool instance API endpoints."""
-
-import logging
-import uuid
-
-import httpx
-from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
-from sqlalchemy.ext.asyncio import AsyncSession
-
-from src.auth.dependencies import get_current_user, get_db_session, get_owned_project
-from src.models.git_repository import GitRepository
-from src.models.project import Project
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.models.user import User
-from src.schemas.tool_instance import CreateInstanceRequest
-from src.services import instance_lifecycle as lifecycle
-from src.services.docker import container as container_svc
-from src.services.docker import tunnel as tunnel_svc
-
-logger = logging.getLogger(__name__)
-router = APIRouter(prefix="/projects", tags=["tool-instances"])
-async def _get_instance(session: AsyncSession, instance_id: uuid.UUID, repo_id: uuid.UUID) -> ToolInstance:
-    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")
-    return instance
-async def _get_repo(session: AsyncSession, repo_id: uuid.UUID, project_id: uuid.UUID) -> GitRepository:
-    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
-# ── Endpoints ──────────────────────────────────────────────────────────────
-
-@router.post("/{project_id}/repositories/{repo_id}/instances")
-async def create_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    data: CreateInstanceRequest,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Create a new tool instance."""
-    repo = await _get_repo(session, repo_id, project_id)
-    tool_type = await session.get(ToolType, uuid.UUID(data.tool_type_id))
-    if tool_type is None:
-        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
-
-    selected_profile = None
-    if data.config_profile_id:
-        from src.models.config_profile import ConfigProfile
-        selected_profile = await session.get(ConfigProfile, uuid.UUID(data.config_profile_id))
-        if selected_profile is None:
-            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config profile not found")
-        if selected_profile.user_id != user.id:
-            raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="config profile does not belong to user")
-
-    instance = await lifecycle.create_new_instance(
-        session, project, repo, tool_type, user, data.display_name, selected_profile,
-        ssh_key_ids=data.ssh_key_ids or None,
-    )
-    return {
-        "id": str(instance.id),
-        "name": instance.name,
-        "display_name": instance.display_name,
-        "tool_type_id": str(instance.tool_type_id),
-        "status": instance.status,
-        "config_profile_id": str(instance.selected_profile_id) if instance.selected_profile_id else None,
-        "ssh_key_ids": instance.ssh_key_ids or [],
-        "created_at": instance.created_at.isoformat(),
-    }
-@router.get("/{project_id}/repositories/{repo_id}/instances")
-async def list_instances(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """List all tool instances for a repository."""
-    await _get_repo(session, repo_id, project_id)
-    from sqlalchemy import select
-    result = await session.execute(
-        select(ToolInstance)
-        .where(ToolInstance.repository_id == repo_id, ToolInstance.owner_id == user.id)
-        .order_by(ToolInstance.created_at.desc())
-    )
-    instances = []
-    for i in result.scalars().all():
-        tt = await session.get(ToolType, i.tool_type_id)
-        instances.append({
-            "id": str(i.id), "name": i.name, "display_name": i.display_name,
-            "tool_type_id": str(i.tool_type_id), "tool_type_name": tt.name if tt else "unknown",
-            "tool_type_interfaces": tt.interfaces if tt else [],
-            "status": i.status, "url": i.url, "port": i.port,
-            "config_profile_id": str(i.selected_profile_id) if i.selected_profile_id else None,
-            "created_at": i.created_at.isoformat(),
-        })
-    return {"instances": instances}
-@router.get("/{project_id}/repositories/{repo_id}/instances/{instance_id}")
-async def get_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get a specific instance with real-time Docker status."""
-    from datetime import datetime
-    instance = await _get_instance(session, instance_id, repo_id)
-    if instance.container_id:
-        docker_status = container_svc.get_container_status(instance.container_id)
-        if docker_status == "running" and instance.status != "running":
-            instance.status = "running"
-            await session.commit()
-        elif docker_status == "exited" and instance.status == "running":
-            instance.status = "stopped"
-            instance.last_stopped_at = datetime.now()
-            await session.commit()
-    return {
-        "id": str(instance.id), "name": instance.name, "display_name": instance.display_name,
-        "tool_type_id": str(instance.tool_type_id), "status": instance.status,
-        "container_id": instance.container_id, "compose_path": instance.compose_path,
-        "url": instance.url, "port": instance.port,
-        "config_profile_id": str(instance.selected_profile_id) if instance.selected_profile_id else None,
-        "last_started_at": instance.last_started_at.isoformat() if instance.last_started_at else None,
-        "last_stopped_at": instance.last_stopped_at.isoformat() if instance.last_stopped_at else None,
-        "created_at": instance.created_at.isoformat(),
-    }
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/start")
-async def start_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Start a tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    return await lifecycle.start_existing_instance(session, instance, user, project_id)
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/stop")
-async def stop_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Stop a running tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    await lifecycle.stop_existing_instance(session, instance)
-    return {"status": instance.status}
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/restart")
-async def restart_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Restart a tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    return await lifecycle.restart_existing_instance(session, instance, user, project_id)
-@router.delete("/{project_id}/repositories/{repo_id}/instances/{instance_id}")
-async def delete_instance(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> None:
-    """Delete a tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    await lifecycle.delete_existing_instance(session, instance)
-@router.get("/{project_id}/repositories/{repo_id}/instances/{instance_id}/logs")
-async def get_instance_logs(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    tail: int = 100,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get container logs for an instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    if not instance.container_id:
-        return {"logs": "No container running"}
-    return {"logs": container_svc.get_container_logs(instance.container_id, tail)}
-@router.post("/{project_id}/repositories/{repo_id}/instances/{instance_id}/recreate-tunnel")
-async def recreate_tunnel_endpoint(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Recreate the temporary tunnel for an instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    if instance.status != "running":
-        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="instance must be running")
-
-    tool_type = await session.get(ToolType, instance.tool_type_id)
-    instance_port = tool_type.default_port if tool_type and tool_type.default_port else 8080
-
-    try:
-        tunnel_info = tunnel_svc.recreate_tunnel(
-            container_name=instance.container_name or instance.name,
-            port=instance_port,
-            old_pid=instance.tunnel_id,
-        )
-        instance.tunnel_id = tunnel_info["pid"]
-        instance.public_url = tunnel_info["url"]
-        instance.url = tunnel_info["url"]
-        await session.commit()
-        return {"status": "healthy", "url": instance.url}
-    except Exception as exc:
-        logger.exception("Failed to recreate tunnel")
-        raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=f"Failed to recreate tunnel: {exc}")
-@router.get("/{project_id}/repositories/{repo_id}/instances/{instance_id}/health")
-async def check_instance_tunnel_health(
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    user: User = Depends(get_current_user),
-    project: Project = Depends(get_owned_project),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Check tunnel health for an instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    if not instance.url or instance.status != "running":
-        return {"healthy": False, "status_code": None, "error": "instance not running"}
-    return tunnel_svc.check_tunnel_health(instance.url)
-@router.api_route(
-    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/proxy/{path:path}",
-    methods=["GET", "POST", "PUT", "DELETE", "PATCH", "HEAD", "OPTIONS"],
-)
-async def proxy_to_instance(
-    request: Request,
-    project_id: uuid.UUID,
-    repo_id: uuid.UUID,
-    instance_id: uuid.UUID,
-    path: str = "",
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> Response:
-    """Proxy HTTP requests to a running tool instance."""
-    instance = await _get_instance(session, instance_id, repo_id)
-    if instance.owner_id != user.id:
-        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="not authorized")
-    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 = str(request.query_params)
-    if query:
-        target_url += f"?{query}"
-
-    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}")
-
-    resp_headers = dict(response.headers)
-    for h in ["content-encoding", "transfer-encoding", "connection"]:
-        resp_headers.pop(h, None)
-    return Response(content=response.content, status_code=response.status_code, headers=resp_headers)
@@ -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"]
@@ -1,5 +1,5 @@
+import base64
 import uuid
-from datetime import datetime

 from cryptography.fernet import Fernet
 from cryptography.hazmat.primitives import serialization
@@ -8,21 +8,26 @@ 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, get_db_session
+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.user import User
-from src.schemas.ssh_key import SSHKeyCreate, SSHKeyResponse
+from src.models import SSHKey
+from src.schemas.project import (
+    SSHKeyCreate,
+    SSHKeyResponse,
+    SignPayloadRequest,
+    SignatureResponse,
+    VerifySignatureRequest,
+    VerifySignatureResponse,
+)

 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])


-
 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()
@@ -63,7 +68,7 @@ def generate_ssh_key_pair() -> tuple[str, str]:
 )
 async def create_ssh_key(
    data: SSHKeyCreate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> SSHKey:
    """Create a new SSH key pair.
@@ -76,6 +81,7 @@ async def create_ssh_key(
    Returns:
        The newly created SSH key with public key exposed.
    """
+    user = await _get_user(session, user_id)
    private_key, public_key = generate_ssh_key_pair()

    fernet = _get_fernet()
@@ -100,7 +106,7 @@ async def create_ssh_key(
    description="List all SSH keys for the authenticated user.",
 )
 async def list_ssh_keys(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> list[SSHKey]:
    """List all SSH keys for the authenticated user.
@@ -112,6 +118,7 @@ async def list_ssh_keys(
    Returns:
        List of SSH keys owned by the user.
    """
+    user = await _get_user(session, user_id)
    result = await session.execute(select(SSHKey).where(SSHKey.user_id == user.id))
    return list(result.scalars().all())

@@ -124,7 +131,7 @@ async def list_ssh_keys(
 )
 async def delete_ssh_key(
    key_id: uuid.UUID,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> None:
    """Delete an SSH key.
@@ -137,9 +144,93 @@ async def delete_ssh_key(
    Returns:
        None with 204 status code.
    """
+    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()
+
+
+@router.post(
+    "/{key_id}/sign",
+    response_model=SignatureResponse,
+    summary="Sign payload",
+    description="Sign a payload using the SSH private key.",
+)
+async def sign_payload(
+    key_id: uuid.UUID,
+    data: SignPayloadRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> SignatureResponse:
+    """Sign a payload with an SSH key.
+
+    Args:
+        key_id: UUID of the SSH key to use for signing.
+        data: Sign request containing the payload string.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Base64-encoded Ed25519 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"
+        )
+
+    fernet = _get_fernet()
+    private_key_pem = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
+
+    private_key = serialization.load_ssh_private_key(
+        private_key_pem.encode(), password=None
+    )
+
+    signature = private_key.sign(data.payload.encode())
+    return SignatureResponse(signature=base64.b64encode(signature).decode())
+
+
+@router.post(
+    "/{key_id}/verify",
+    response_model=VerifySignatureResponse,
+    summary="Verify signature",
+    description="Verify a signature against a payload using the SSH public key.",
+)
+async def verify_signature(
+    key_id: uuid.UUID,
+    data: VerifySignatureRequest,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> VerifySignatureResponse:
+    """Verify a signature with an SSH key's public key.
+
+    Args:
+        key_id: UUID of the SSH key to use for verification.
+        data: Verify request containing payload and base64-encoded signature.
+        user_id: ID of the authenticated user.
+        session: Database session.
+
+    Returns:
+        Whether the signature is valid.
+    """
+    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"
+        )
+
+    public_key = serialization.load_ssh_public_key(ssh_key.public_key.encode())
+
+    try:
+        signature = base64.b64decode(data.signature)
+        public_key.verify(signature, data.payload.encode())
+        return VerifySignatureResponse(valid=True)
+    except Exception:
+        return VerifySignatureResponse(valid=False)
@@ -2,13 +2,10 @@ import uuid
 from pathlib import Path

 from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
-from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession

-from src.auth.dependencies import get_current_user, get_db_session
-from src.models.tool_instance import ToolInstance
+from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.user import User
-from src.schemas.tool_instance import SessionItemResponse, SessionListResponse
 from src.schemas.user import UserProfileResponse, UserProfileUpdate

 router = APIRouter(prefix="/users", tags=["users"])
@@ -26,7 +23,7 @@ MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
    description="Retrieve the profile of the currently authenticated user.",
 )
 async def get_profile(
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> User:
    """Get the current user's profile.
@@ -38,7 +35,7 @@ async def get_profile(
    Returns:
        The user's profile information.
    """
-    return user
+    return await _get_user(session, user_id)


@router.put(
@@ -49,7 +46,7 @@ async def get_profile(
 )
 async def update_profile(
    data: UserProfileUpdate,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> User:
    """Update the current user's profile.
@@ -62,6 +59,7 @@ async def update_profile(
    Returns:
        The updated user profile.
    """
+    user = await _get_user(session, user_id)

    if data.name is not None:
        if len(data.name.strip()) == 0:
@@ -90,7 +88,7 @@ async def update_profile(
 )
 async def upload_avatar(
    file: UploadFile,
-    user: User = Depends(get_current_user),
+    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> User:
    """Upload a profile avatar image.
@@ -103,6 +101,7 @@ async def upload_avatar(
    Returns:
        The updated user profile with new avatar URL.
    """
+    user = await _get_user(session, user_id)

    if file.content_type not in ALLOWED_CONTENT_TYPES:
        raise HTTPException(
@@ -137,41 +136,3 @@ async def upload_avatar(
    await session.commit()
    await session.refresh(user)
    return user
-
-
-@router.get(
-    "/me/sessions",
-    response_model=SessionListResponse,
-    summary="Get current user sessions",
-    description="Retrieve all tool instances (sessions) for the authenticated user.",
-)
-async def get_user_sessions(
-    user: User = Depends(get_current_user),
-    session: AsyncSession = Depends(get_db_session),
-) -> SessionListResponse:
-    """Return all tool instances for the current user with related names."""
-    result = await session.execute(
-        select(ToolInstance)
-        .where(ToolInstance.owner_id == user.id)
-        .order_by(ToolInstance.created_at.desc())
-    )
-    instances = result.scalars().all()
-
-    sessions = [
-        SessionItemResponse(
-            id=str(inst.id),
-            display_name=inst.display_name,
-            tool_type_name=inst.tool_type.display_name if inst.tool_type else "Unknown",
-            tool_icon=None,
-            tool_type_interfaces=inst.tool_type.interfaces if inst.tool_type else [],
-            repository_name=inst.repository.name if inst.repository else "Unknown",
-            repository_id=str(inst.repository_id),
-            project_name=inst.project.name if inst.project else "Unknown",
-            project_id=str(inst.project_id),
-            status=inst.status,
-            url=inst.url,
-        )
-        for inst in instances
-    ]
-
-    return SessionListResponse(sessions=sessions)
@@ -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.services.file_service import FileService
+from src.models import Workspace
+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.services.git_operations import GitOperations
+from src.models import Workspace
+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.tool_instance import ToolInstance
-from src.models.workspace import Workspace
-from src.services.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
+from src.models import GitRepository
+from src.models import Project
+from src.models import ToolInstance
+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.project_id,
-            GitRepository.ssh_key_id.label("repo_ssh_key_id"),
+            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(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_name": repo_name or "",
-            "repo_ssh_key_id": str(ssh_key_id) if ssh_key_id else None,
-            "project_id": str(project_id) if project_id else "",
-            "project_name": "",
+            "repo_id": str(repo.id),
+            "repo_name": repo.name or "",
+            "repo_ssh_key_id": str(repo.ssh_key_id) if repo.ssh_key_id else None,
+            "project_id": str(repo.project_id) if repo.project_id else "",
+            "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,
-            detail="Workspace name already exists for this repository",
+            status_code=500,
+            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,
-            detail="Workspace name already exists for this repository",
+            status_code=500,
+            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