fix: use host bind mount for repos so tool instances can access workspace files

Replace named Docker volume (repo_data) with bind mount (/data/repos) in both development and production compose files. The named volume trapped repo files inside the API container; tool instances started via Docker socket on the host could not see them, causing /workspace to mount as an empty directory. Also fix 6 pre-existing test failures in test_tool_instances_legacy.py caused by get_container_id/get_container_name moving to docker.py and new helpers (_ensure_web_bind_address, _ensure_container_name_in_compose) being added. - docker-compose.yml: repo_data:/data/repos -> /data/repos:/data/repos - docker-compose.traefik.yml: same change + remove repo_data volume decl - tests: update patch targets and add missing mock parameters Quality gates: pytest test_tool_instances_legacy.py (10 passed)
2026-06-02 12:47:14 +02:00
1170 changed files with 19966 additions and 53528 deletions
@@ -1,3 +1,3 @@
 {
-  "fingerprint": "639c16d45210921c3c8ece071ef18bbe0c426ea2"
+  "fingerprint": "fdea8a74bb4c7449c01c4bd61646c895b10ede78"
 }
@@ -1,13 +1,14 @@
-# Skill Registry — workspace
+# Skill Registry — headquarter
 <!-- Auto-generated by gentle-pi extensions/skill-registry.ts. Run /skill-registry:refresh to regenerate. -->
-Last updated: 2026-06-05
+Last updated: 2026-05-28
 ## Sources scanned
 - .opencode/skills
 - .claude/skills
 - /home/alex/.config/opencode/skills
 ## Contract
@@ -19,11 +20,13 @@ Last updated: 2026-06-05
 | Skill | Trigger / description | Scope | Path |
 | --- | --- | --- | --- |
-| `openspec-apply-change` | Implement tasks from an OpenSpec change. Use when the user wants to start implementing, continue implementation, or work through tasks. | project | `/workspace/.opencode/skills/openspec-apply-change/SKILL.md` |
+| `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-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 | `/workspace/.opencode/skills/openspec-archive-change/SKILL.md` |
+| `openspec` | Use OpenSpec as the source of truth for planning, implementation, verification, and archive discipline. | user | `/home/alex/.config/opencode/skills/openspec/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 | `/workspace/.opencode/skills/openspec-explore/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-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 | `/workspace/.opencode/skills/openspec-propose/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` |
-| `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 | `/workspace/.claude/skills/sift-backlog/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` |
 ## Loading protocol
@@ -1,20 +0,0 @@
 # .claude (index)
 dir: .claude
 ## role
 Configuration directory for Claude AI assistant integration 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
 -
@@ -1,18 +0,0 @@
 # .claude
 dir: .claude
 index: .claude/.pi-map.index.md
 ## role
 Configuration directory for Claude AI assistant integration and custom instructions.
 ## files
 ## arch
 Project-specific AI tooling configuration using convention-based file organization for assistant context and behavior customization.
 ## tags
 -
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,20 +0,0 @@
 # .claude/skills (index)
 dir: .claude/skills
 ## role
 Contains reusable AI skill definitions and prompt templates that configure Claude's specialized capabilities for specific development tasks.
 ## 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
 -
@@ -1,18 +0,0 @@
 # .claude/skills
 dir: .claude/skills
 index: .claude/skills/.pi-map.index.md
 ## role
 Contains reusable AI skill definitions and prompt templates that configure Claude's specialized capabilities for specific development tasks.
 ## files
 ## arch
 Modular skill-based architecture using declarative configuration files (likely YAML/JSON) to define context-specific behaviors, tool access patterns, and system prompts for different operational modes.
 ## tags
 -
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,19 +0,0 @@
 # .claude/skills/sift-backlog (index)
 dir: .claude/skills/sift-backlog
 ## role
 Defines 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
 -
@@ -1,19 +0,0 @@
 # .claude/skills/sift-backlog
 dir: .claude/skills/sift-backlog
 index: .claude/skills/sift-backlog/.pi-map.index.md
 ## role
 Defines 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 (custom CLI tool), task management system, plan management system
 ## arch
 Documentation-driven skill definition using structured markdown with command specifications, workflow stages, and integration patterns for Claude CLI tooling.
 ## tags
 skill, defines, workflow, triaging, organizing, activating, backlog, tasks
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -17,7 +17,6 @@ __pycache__/
 *.so
 .python-version
 .venv/
 .venv-test/
 venv/
 env/
 .pytest_cache/
@@ -55,6 +54,3 @@ Thumbs.db
 .atl/
 .sisyphus/
 .pi-lens/
 minerv3/
 .cache/
 openspec-audit-report.md
@@ -1,23 +0,0 @@
 # .opencode (index)
 dir: .opencode
 ## role
 Hidden directory for OpenCode IDE/editor configuration and workspace metadata
 ## 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
 -
@@ -1,18 +0,0 @@
 # .opencode
 dir: .opencode
 index: .opencode/.pi-map.index.md
 ## role
 Hidden directory for OpenCode IDE/editor configuration and workspace metadata
 ## files
 ## arch
 IDE-specific dot-directory pattern, no active code architecture; stores tool preferences and ephemeral state
 ## tags
 -
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,22 +0,0 @@
 # .opencode/commands (index)
 dir: .opencode/commands
 ## role
 Defines experimental workflow skills and AI assistant stances for an OpenSpec-based development system with structured change management.
 ## 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
 -
@@ -1,22 +0,0 @@
 # .opencode/commands
 dir: .opencode/commands
 index: .opencode/commands/.pi-map.index.md
 ## role
 Defines experimental workflow skills and AI assistant stances for an OpenSpec-based development system with structured change management.
 ## files
 - opsx-apply.md | Defines an experimental workflow skill for implementing tasks from an OpenSpec change through a structured, interactive process with CLI integration and progress tracking. | dep: openspec CLI, AskUserQuestion tool, filesystem (for reading context files)
 - opsx-archive.md | Defines a workflow for archiving completed changes in an experimental openspec-based development system | dep: openspec CLI, AskUserQuestion tool, Task tool, Skill tool, filesystem (mkdir, mv), JSON parsing
 - opsx-explore.md | Defines the "explore mode" stance for an AI assistant - a thinking/discovery mode for investigating problems and clarifying requirements without implementing code | dep: OpenSpec system
 - opsx-propose.md | Defines a workflow for proposing new changes in the openspec system by creating a change directory and generating all required artifacts (proposal.md, design.md, tasks.md) in dependency order | dep: openspec CLI, AskUserQuestion tool, TodoWrite tool, JSON parsing
 ## arch
 Markdown-based command definitions using a workflow pattern with interactive CLI integration, progress tracking, and dependency-ordered artifact generation across explore/propose/apply/archive lifecycle phases.
 ## tags
 opsx, defines, workflow, openspec, openspec cli, askuserquestion tool, explore, experimental
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,29 +0,0 @@
 # .opencode/skills (index)
 dir: .opencode/skills
 ## role
 Contains reusable AI skill modules that provide specialized capabilities for the OpenCode assistant.
 ## 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
 -
@@ -1,18 +0,0 @@
 # .opencode/skills
 dir: .opencode/skills
 index: .opencode/skills/.pi-map.index.md
 ## role
 Contains reusable AI skill modules that provide specialized capabilities for the OpenCode assistant.
 ## files
 ## arch
 Modular plugin-based architecture where each skill is a self-contained module with defined interfaces, enabling dynamic loading and composition of AI capabilities.
 ## tags
 -
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,19 +0,0 @@
 # .opencode/skills/openspec-apply-change (index)
 dir: .opencode/skills/openspec-apply-change
 ## role
 Defines an AI assistant skill that implements OpenSpec changes through a spec-driven workflow with structured planning, validation, and execution phases.
 ## 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
 -
@@ -1,19 +0,0 @@
 # .opencode/skills/openspec-apply-change
 dir: .opencode/skills/openspec-apply-change
 index: .opencode/skills/openspec-apply-change/.pi-map.index.md
 ## role
 Defines an AI assistant skill that implements OpenSpec changes through a spec-driven workflow with structured planning, validation, and execution phases.
 ## files
 - SKILL.md | Defines an AI assistant skill for implementing tasks from an OpenSpec change using a spec-driven workflow | dep: openspec CLI, AskUserQuestion tool, filesystem access
 ## arch
 Template-based skill definition using markdown documentation with structured workflow phases (planning, validation, execution) and integration points for external tools (OpenSpec CLI, OpenCode agent).
 ## tags
 skill, defines, assistant, implementing, tasks, openspec, change, spec
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,19 +0,0 @@
 # .opencode/skills/openspec-archive-change (index)
 dir: .opencode/skills/openspec-archive-change
 ## role
 Provides a reusable automation skill for archiving completed experimental changes via 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
 -
@@ -1,19 +0,0 @@
 # .opencode/skills/openspec-archive-change
 dir: .opencode/skills/openspec-archive-change
 index: .opencode/skills/openspec-archive-change/.pi-map.index.md
 ## role
 Provides a reusable automation skill for archiving completed experimental changes via 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, file system (mkdir, mv, read), JSON parsing
 ## arch
 Skill-based modular automation pattern using markdown-defined CLI operations with structured metadata and command templates
 ## tags
 skill, defines, archiving, completed, changes, experimental, workflow, openspec
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,19 +0,0 @@
 # .opencode/skills/openspec-explore (index)
 dir: .opencode/skills/openspec-explore
 ## role
 Defines a conversational AI skill/persona for "explore mode" that serves as a thinking partner for exploring ideas, investigating problems, and clarifying requirements without implementing code.
 ## 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
 -
@@ -1,19 +0,0 @@
 # .opencode/skills/openspec-explore
 dir: .opencode/skills/openspec-explore
 index: .opencode/skills/openspec-explore/.pi-map.index.md
 ## role
 Defines a conversational AI skill/persona for "explore mode" that serves as a thinking partner for exploring ideas, investigating problems, and clarifying requirements without implementing code.
 ## files
 - SKILL.md | Defines a conversational AI skill/persona for "explore mode" - a thinking partner for exploring ideas, investigating problems, and clarifying requirements without implementing code. | dep: openspec CLI
 ## arch
 Single-file skill definition using markdown-based persona specification with structured sections for description, usage guidelines, and behavioral constraints.
 ## tags
 skill, defines, conversational, persona, explore, mode, thinking, partner
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,19 +0,0 @@
 # .opencode/skills/openspec-propose (index)
 dir: .opencode/skills/openspec-propose
 ## role
 Provides a structured workflow skill for proposing new changes using the openspec CLI with artifact generation in dependency order.
 ## 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
 -
@@ -1,19 +0,0 @@
 # .opencode/skills/openspec-propose
 dir: .opencode/skills/openspec-propose
 index: .opencode/skills/openspec-propose/.pi-map.index.md
 ## role
 Provides a structured workflow skill for proposing new changes using the openspec CLI with artifact generation in dependency order.
 ## files
 - SKILL.md | Defines a structured workflow for proposing new changes using the openspec CLI, generating proposal, design, and task artifacts in dependency order. | dep: openspec CLI, AskUserQuestion tool, TodoWrite tool
 ## arch
 Template-based skill definition using markdown documentation with sequential artifact generation (proposal → design → tasks) following dependency ordering.
 ## tags
 skill, defines, structured, workflow, proposing, new, changes, openspec
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,82 +0,0 @@
 # . (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
 Infrastructure and deployment configuration for a self-hosted project management platform with OAuth2 authentication, providing Docker Compose orchestration, environment templates, and development tooling.
 ## 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
 - minerv3
  index: minerv3/.pi-map.index.md
  map: minerv3/.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
 ## links
 index: ./.pi-map.index.md
 map: ./.pi-map.md
 ## workflows
 -
 ## dirty
 -
@@ -1,42 +0,0 @@
 # .
 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
 Infrastructure and deployment configuration for a self-hosted project management platform with OAuth2 authentication, providing Docker Compose orchestration, environment templates, and development tooling.
 ## files
 - .env.example | Provides a template of environment variables for configuring a Headquarter application with PostgreSQL, Redis, Authentik SSO, and Docker/Traefik deployment
 - .gitignore | Specifies files and directories for Git to ignore across a multi-language project with Python, Node, and custom tooling | dep: Git
 - AGENTS.md | Defines operational rules, workflows, and constraints for AI agents working within an OpenSpec-driven software development project. | dep: OpenSpec, superpowers, git, docker compose, conventional commits
 - CHANGELOG.md | Documents version history and notable changes for a Git-based project management web application
 - Makefile | Provides standard development commands for containerized web application lifecycle management via Docker Compose | dep: docker compose, alembic, pytest, ruff, mypy, playwright, npm, postgres, redis
 - README.md | A self-hosted platform for managing 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, Git
 - docker-compose.traefik.yml | Deploys a multi-service web application (frontend, API, PostgreSQL, Redis) behind an existing Traefik reverse proxy with TLS termination and environment-configurable domains. | dep: docker, traefik, postgres, redis, authentik, docker-compose
 - docker-compose.yml | Defines a multi-service Docker Compose stack with PostgreSQL, Redis, API backend, and web frontend services for a "headquarter" application | dep: Docker, PostgreSQL, Redis, Vite, asyncpg, nginx
 - progress.md | Tracks completed and remaining tasks for a backend-frontend code refactoring project organized in 7 phases
 - swap-pane | Empty file with no functionality
 ## arch
 Containerized microservices architecture using Docker Compose with PostgreSQL and Redis data layers, Traefik reverse proxy for TLS/ingress, multi-stage builds for Node.js frontend and Python backend, and environment-driven configuration management.
 ## tags
 docker, redis, git, application, postgresql, compose, traefik, project
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,23 +0,0 @@
 # .stoneforge (index)
 dir: .stoneforge
 ## role
 Internal configuration and state tracking directory for the Stoneforge application
 ## 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
 -
@@ -1,21 +0,0 @@
 # .stoneforge
 dir: .stoneforge
 index: .stoneforge/.pi-map.index.md
 ## role
 Internal configuration and state tracking directory for the Stoneforge application
 ## files
 - .dashboard-opened | Stores timestamp and identifier data for tracking when a dashboard was opened
 - .gitignore | Specifies files and patterns for Git to ignore in version control
 - config.yaml | Configuration file for the Stoneforge application defining database, sync, playbook, identity, merge, workflow, and agent settings.
 ## arch
 Simple dot-directory pattern storing metadata (.dashboard-opened), version control exclusions (.gitignore), and hierarchical YAML configuration (config.yaml) with domain-separated settings
 ## tags
 config, stores, timestamp, identifier, data, tracking, dashboard, was
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,20 +0,0 @@
 # .stoneforge/sync (index)
 dir: .stoneforge/sync
 ## role
 Persists distributed task execution state by storing dependency graphs and ephemeral worker agent records for a collaborative workflow 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
 -
@@ -1,20 +0,0 @@
 # .stoneforge/sync
 dir: .stoneforge/sync
 index: .stoneforge/sync/.pi-map.index.md
 ## role
 Persists distributed task execution state by storing dependency graphs and ephemeral worker agent records for a collaborative workflow system.
 ## files
 - dependencies.jsonl | Stores a sequence of dependency relationships between entities in JSON Lines format, tracking parent-child, blocking, and reply relationships with timestamps and creators.
 - elements.jsonl | Stores JSONL records of ephemeral worker agents with their session history, worktree assignments, and lifecycle metadata for a distributed task execution system.
 ## arch
 Event-sourced JSONL append-only logs with entity-relationship modeling (parent-child, blocking, reply) and session-based worker lifecycle tracking.
 ## tags
 stores, relationships, dependencies, elements, sequence, dependency, entities, json
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -75,7 +75,6 @@ Do not:
 * Introduce new dependencies without clear justification.
 * Treat existing code as more authoritative than OpenSpec for intended behavior.
 * Decide product behavior silently when the spec is unclear.
 * Run `docker compose` commands (build, up, down, etc.) without explicit user approval and proper isolation (e.g., feature branches, separate worktrees, or staged rollouts). Docker Compose operations are deployment-level changes that can affect running services, shared volumes, and network state. Always ask first.
 If scope must change, propose an OpenSpec update first.
@@ -1,23 +0,0 @@
 # apps (index)
 dir: apps
 ## role
 Container for deployable application entry points and top-level configurations in the project.
 ## 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
 -
@@ -1,18 +0,0 @@
 # apps
 dir: apps
 index: apps/.pi-map.index.md
 ## role
 Container for deployable application entry points and top-level configurations in the project.
 ## files
 ## arch
 Monorepo-style directory structure housing independently runnable applications that share common libraries or modules, typically with per-app configuration, dependencies, and build targets.
 ## tags
 -
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -1,42 +0,0 @@
 # 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/
@@ -1,51 +0,0 @@
 # apps/api (index)
 dir: apps/api
 ## role
 Self-hosted FastAPI backend API that manages projects, git repositories, and development tools by orchestrating Docker instances for remote development environments.
 ## 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/.venv-test
  index: apps/api/.venv-test/.pi-map.index.md
  map: apps/api/.venv-test/.pi-map.md
 - apps/api/alembic
  index: apps/api/alembic/.pi-map.index.md
  map: apps/api/alembic/.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
 -
@@ -1,25 +0,0 @@
 # apps/api
 dir: apps/api
 index: apps/api/.pi-map.index.md
 ## role
 Self-hosted FastAPI backend API that manages projects, git repositories, and development tools by orchestrating Docker instances for remote development environments.
 ## files
 - .dockerignore | Specifies files and directories to exclude from Docker build context to reduce image size and avoid copying unnecessary files into containers. | dep: Docker
 - Dockerfile | Multi-stage Docker build for a Python application with Docker socket access, Cloudflare tunneling, and database dependency waiting | dep: python:3.11-slim, gcc, libpq-dev, docker-ce-cli, docker-compose-plugin, cloudflared, uvicorn, pyproject.toml dependencies
 - README.md | Documentation for a self-hosted FastAPI backend API that manages projects, git repositories, and development tools via Docker instances. | dep: FastAPI, SQLAlchemy, PostgreSQL, asyncpg, Alembic, Docker, Docker Compose, Authentik, uvicorn, pytest, ruff, mypy
 - alembic.ini | Configuration file for Alembic database migration tool connecting to a PostgreSQL database with async driver | dep: alembic, sqlalchemy, asyncpg, PostgreSQL
 - pyproject.toml | Defines Python project metadata, dependencies, and tool configurations for a FastAPI-based backend API called "headquarter-api" | dep: fastapi, uvicorn, sqlalchemy, asyncpg, alembic, pydantic, pydantic-settings, python-multipart, httpx, structlog, cryptography, pytest, pytest-asyncio, mypy, ruff, aiosqlite
 - uv.lock | Lock file for the uv Python package manager that pins exact dependency versions and their artifact hashes for reproducible installations | dep: uv, Python 3.11+, aiosqlite, alembic, annotated-doc, annotated-types, anyio, ast-serialize, asyncpg, and many other PyPI packages
 - wait-for-db.sh | Wait for a PostgreSQL database to become available before executing a command, with configurable retry logic. | dep: nc (netcat), sh (POSIX shell), sleep
 ## arch
 Async Python backend using FastAPI with PostgreSQL (asyncpg), Alembic migrations, uv package management, multi-stage Docker builds with Docker-in-Docker socket access, and Cloudflare tunneling for secure external connectivity.
 ## tags
 docker, alembic, python, database, fastapi, postgresql, asyncpg, uvicorn
 ## symbols
 -
 ## workflows
 -
 ## dirty
 -
@@ -50,8 +50,8 @@ ENV PATH=/root/.local/bin:$PATH
 # Copy application code
 COPY --chown=appuser:appgroup . .
-# Create directories for repo, instance, and workspace storage
+# Create directories for repo and instance storage
-RUN mkdir -p /data/repos /data/instances /data/working-copies && chown -R appuser:appgroup /data
+RUN mkdir -p /data/repos /data/instances && chown -R appuser:appgroup /data
 # Copy wait-for-db script
 COPY wait-for-db.sh /usr/local/bin/wait-for-db.sh
@@ -1,25 +0,0 @@
 # apps/api/alembic (index)
 dir: apps/api/alembic
 ## role
 Database migration infrastructure for the API application, providing 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
 -
@@ -1,30 +0,0 @@
 # apps/api/alembic
 dir: apps/api/alembic
 index: apps/api/alembic/.pi-map.index.md
 ## role
 Database migration infrastructure for the API application, providing version-controlled schema changes with async SQLAlchemy support.
 ## files
 - env.py | Configures Alembic database migration environment with async SQLAlchemy support for a project. | 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 upgrade/downgrade functions for SQLAlchemy schema migrations | dep: alembic, sqlalchemy
 ## arch
 Alembic migration framework with Mako templating for generating migration scripts, configured for async SQLAlchemy operations.
 ## 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
 -
@@ -1,77 +0,0 @@
 # apps/api/alembic/versions (index)
 dir: apps/api/alembic/versions
 ## role
 Database schema version control and migration management for the API application, tracking incremental schema changes from initial tables through advanced features like workspaces, manifests, and monitoring.
 ## 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
 - 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
 -
@@ -1,82 +0,0 @@
 # apps/api/alembic/versions
 dir: apps/api/alembic/versions
 index: apps/api/alembic/versions/.pi-map.index.md
 ## role
 Database schema version control and migration management for the API application, tracking incremental schema changes from initial tables through advanced features like workspaces, manifests, and monitoring.
 ## files
 - 0001_initial_schema.py | Defines the initial database schema migration creating five tables (users, ssh_keys, projects, git_repositories, user_configs) with relationships, indexes, and constraints using Alembic. | 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, postgresql dialect
 - 0002_refresh_tokens.py | Alembic database migration that creates a refresh_tokens table with indexes for user authentication token 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 linked to users | 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 versioning columns for a tool management system. | 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 columns for tracking deployed tool instances, their status, container info, and foreign key relationships to tool_types, git_repositories, projects, and users. | 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 keys, foreign key relationships, and indexes for storing user/project tool configuration settings. | 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, postgresql dialect
 - 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 null default_port values for existing tool types and then 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, includes, mounts tables and links tool instances to profiles with defensive idempotent 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: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 | Alembic database migration that adds 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 (project_id, tool_type_id, environment_variables, etc.) to config_profiles table and restructures config_mounts table (renaming mount_path to target_path, adding mode/files, removing content/source_profile_id). | 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 into a single history line | 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 `interface_type` string and `requires_port` boolean columns in the `tool_types` table, with dialect-specific data migration for PostgreSQL and SQLite. | 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, postgresql (dialect)
 - 069d3da4dc9b_add_ssh_key_id_to_config_profiles.py | Alembic database migration that adds a nullable UUID foreign key column `ssh_key_id` to the `config_profiles` table referencing `ssh_keys.id` with SET NULL on delete | 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 | Alembic database migration that adds a new "pi-agent" tool type with terminal-based Docker environment for the Pi coding agent | 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 to remove the `is_builtin` column from the `tool_types` table | 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` text 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 foreign key column to tool_instances for managing user configuration profiles. | 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, postgresql dialect
 - 2026_05_26_add_git_mounts.py | Alembic database migration that adds 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 64 characters. | 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 | Alembic database migration that creates monitoring tables (instance_events and health_checks) with indexes for tracking tool instance events and health checks | 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 tracking columns and foreign key to tool_instances | 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 existing tool_types and tool_instances tables, and seeds initial data with a base Ubuntu image and pi-agent manifest while migrating the legacy pi-agent from Dockerfile templates to the new manifest system. | 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 `tool_configs` and `config_folders` tables with conditional existence checks and full downgrade recreation | 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 | Alembic database migration that creates a notifications table with user-linked, categorized, severity-graded messages supporting read/dismissed tracking and optimized querying 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 column named ssh_key_ids 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 and instance files by replacing broken `--host` flags with correct `--bind-addr 0.0.0.0:port` configurations | 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 updates code-server and jupyter-notebook tool type compose templates to bind to 0.0.0.0 | 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 flags from LinuxServer.io 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, pathlib.Path, information_schema
 - 2026_05_29_remove_ssh_keys_mount_from_manifest.py | Alembic database migration that removes (or restores) the ssh_keys mount from a JSON manifest stored in the tool_definition_manifests table for the pi-agent tool definition. | 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 `tool_instances` table nullable to support workspace-first cleanup workflow. | 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 | Alembic database migration that adds a `home_directory` column to `tool_types` table and updates template strings to use a configurable workspace path instead of hardcoded `/workspace` | 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 updates the pi-agent tool definition manifest to mount repositories under the home directory instead of /workspace | 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 synthesizes them via compile_compose instead | 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
 - 398082499c30_add_tool_config_fields.py | Alembic database migration that adds five new columns (port_override, start_command, working_directory, environment_variables, volumes) to the tool_configs table with a port range check 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 database migration that merges two parallel revision branches (removing is_builtin and adding config_profiles) into a single history line | exp: func:upgrade() → None, func:downgrade() → None | dep: alembic
 - 86cec91fdb00_merge_profile_resolver_and_workspaces_.py | Alembic database migration that merges two divergent migration branches (profile resolver and workspaces) into a single 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 the pi-agent manifest stored in tool_definition_manifests table | 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 user-owned configuration folders supporting JSONB file storage and project overrides | 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, sqlalchemy.dialects.postgresql
 - af8512103d67_add_tool_type_fields.py | Alembic database migration that adds new columns (definition_type, dockerfile_template, build_context, readiness_probe) to the tool_types table with a CHECK constraint on definition_type. | 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 prior revisions (single_interface and clone_mode) into a single migration path | 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 divergent migration branches (home directory cleanup and pi agent mount cleanup) into a single revision history | exp: func:upgrade() → None, func:downgrade() → None | dep: alembic
 ## arch
 Linear and branched migration history using Alembic's revision system with merge points to reconcile divergent branches; migrations use declarative SQLAlchemy operations with defensive idempotent checks, conditional existence guards, dialect-specific handling (PostgreSQL/SQLite), and in-place data migrations for template/schema evolution.
 ## tags
 column, table, call:op.drop, alembic, downgrade, upgrade, 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
 -
@@ -1,204 +0,0 @@
 """add config profiles, includes, mounts, and tool instance profile selection
 Revision ID: 0013_add_config_profiles
 Revises: 0012_default_port_req
 Create Date: 2026-05-24 12:00:00.000000
 """
 from collections.abc import Sequence
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import postgresql
 # revision identifiers, used by Alembic.
 revision: str = "0013_add_config_profiles"
 down_revision: str | None = "0012_default_port_req"
 branch_labels: str | Sequence[str] | None = None
 depends_on: str | Sequence[str] | None = None
 def _table_exists(table_name: str) -> bool:
    return sa.inspect(op.get_bind()).has_table(table_name)
 def _column_exists(table_name: str, column_name: str) -> bool:
    if not _table_exists(table_name):
        return False
    return column_name in {
        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
    }
 def _index_exists(table_name: str, index_name: str) -> bool:
    if not _table_exists(table_name):
        return False
    return index_name in {
        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
    }
 def _foreign_key_exists(
    table_name: str,
    constrained_columns: list[str],
    referred_table: str,
 ) -> bool:
    if not _table_exists(table_name):
        return False
    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
        if (
            foreign_key.get("constrained_columns") == constrained_columns
            and foreign_key.get("referred_table") == referred_table
        ):
            return True
    return False
 def upgrade() -> None:
    # Earlier branches may already have created config_profiles. Keep this
    # migration defensive so databases can converge onto the current graph.
    if not _table_exists("config_profiles"):
        op.create_table(
            "config_profiles",
            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
            sa.Column("user_id", postgresql.UUID(as_uuid=True), nullable=False),
            sa.Column("name", sa.String(length=255), nullable=False),
            sa.Column("description", sa.Text(), nullable=True),
            sa.Column(
                "created_at",
                sa.DateTime(timezone=True),
                server_default=sa.text("NOW()"),
                nullable=False,
            ),
            sa.Column(
                "updated_at",
                sa.DateTime(timezone=True),
                server_default=sa.text("NOW()"),
                nullable=False,
            ),
            sa.ForeignKeyConstraint(["user_id"], ["users.id"], ondelete="CASCADE"),
            sa.PrimaryKeyConstraint("id"),
            sa.UniqueConstraint(
                "user_id", "name", name="uq_config_profiles_user_name"
            ),
        )
    if not _index_exists("config_profiles", "idx_config_profiles_user"):
        op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
    if not _table_exists("config_includes"):
        op.create_table(
            "config_includes",
            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
            sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
            sa.Column(
                "included_profile_id", postgresql.UUID(as_uuid=True), nullable=False
            ),
            sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
            sa.Column(
                "created_at",
                sa.DateTime(timezone=True),
                server_default=sa.text("NOW()"),
                nullable=False,
            ),
            sa.Column(
                "updated_at",
                sa.DateTime(timezone=True),
                server_default=sa.text("NOW()"),
                nullable=False,
            ),
            sa.ForeignKeyConstraint(
                ["profile_id"], ["config_profiles.id"], ondelete="CASCADE"
            ),
            sa.ForeignKeyConstraint(
                ["included_profile_id"],
                ["config_profiles.id"],
                ondelete="CASCADE",
            ),
            sa.PrimaryKeyConstraint("id"),
            sa.UniqueConstraint(
                "profile_id", "included_profile_id", name="uq_config_includes_pair"
            ),
        )
    if not _index_exists("config_includes", "idx_config_includes_profile"):
        op.create_index("idx_config_includes_profile", "config_includes", ["profile_id"])
    if not _index_exists("config_includes", "idx_config_includes_included"):
        op.create_index(
            "idx_config_includes_included", "config_includes", ["included_profile_id"]
        )
    if not _table_exists("config_mounts"):
        op.create_table(
            "config_mounts",
            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
            sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
            sa.Column("mount_path", sa.String(length=1024), nullable=False),
            sa.Column("content", sa.Text(), nullable=True),
            sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
            sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
            sa.Column(
                "created_at",
                sa.DateTime(timezone=True),
                server_default=sa.text("NOW()"),
                nullable=False,
            ),
            sa.Column(
                "updated_at",
                sa.DateTime(timezone=True),
                server_default=sa.text("NOW()"),
                nullable=False,
            ),
            sa.ForeignKeyConstraint(
                ["profile_id"], ["config_profiles.id"], ondelete="CASCADE"
            ),
            sa.ForeignKeyConstraint(
                ["source_profile_id"], ["config_profiles.id"], ondelete="SET NULL"
            ),
            sa.PrimaryKeyConstraint("id"),
        )
    if not _index_exists("config_mounts", "idx_config_mounts_profile"):
        op.create_index("idx_config_mounts_profile", "config_mounts", ["profile_id"])
    if not _column_exists("tool_instances", "selected_profile_id"):
        op.add_column(
            "tool_instances",
            sa.Column("selected_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
        )
    if not _foreign_key_exists(
        "tool_instances", ["selected_profile_id"], "config_profiles"
    ):
        op.create_foreign_key(
            "fk_tool_instances_selected_profile",
            "tool_instances",
            "config_profiles",
            ["selected_profile_id"],
            ["id"],
            ondelete="SET NULL",
        )
    if not _index_exists("tool_instances", "idx_tool_instances_selected_profile"):
        op.create_index(
            "idx_tool_instances_selected_profile",
            "tool_instances",
            ["selected_profile_id"],
        )
 def downgrade() -> None:
    # Remove selected_profile_id from tool_instances
    op.drop_index("idx_tool_instances_selected_profile", table_name="tool_instances")
    op.drop_constraint(
        "fk_tool_instances_selected_profile", "tool_instances", type_="foreignkey"
    )
    op.drop_column("tool_instances", "selected_profile_id")
    # Drop config_mounts
    op.drop_index("idx_config_mounts_profile", table_name="config_mounts")
    op.drop_table("config_mounts")
    # Drop config_includes
    op.drop_index("idx_config_includes_included", table_name="config_includes")
    op.drop_index("idx_config_includes_profile", table_name="config_includes")
    op.drop_table("config_includes")
    # Drop config_profiles
    op.drop_index("idx_config_profiles_user", table_name="config_profiles")
    op.drop_table("config_profiles")
@@ -1,180 +0,0 @@
 """add profile resolver fields to config profiles and mounts
 Revision ID: 0014_add_profile_resolver_fields
 Revises: 0013_add_config_profiles
 Create Date: 2026-05-24 14:00:00.000000
 """
 from collections.abc import Sequence
 from alembic import op
 import sqlalchemy as sa
 from sqlalchemy.dialects import postgresql
 # revision identifiers, used by Alembic.
 revision: str = "0014_add_profile_resolver_fields"
 down_revision: str | None = "0013_add_config_profiles"
 branch_labels: str | Sequence[str] | None = None
 depends_on: str | Sequence[str] | None = None
 def _table_exists(table_name: str) -> bool:
    return sa.inspect(op.get_bind()).has_table(table_name)
 def _column_exists(table_name: str, column_name: str) -> bool:
    if not _table_exists(table_name):
        return False
    return column_name in {
        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
    }
 def _index_exists(table_name: str, index_name: str) -> bool:
    if not _table_exists(table_name):
        return False
    return index_name in {
        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
    }
 def _foreign_key_exists(
    table_name: str,
    constrained_columns: list[str],
    referred_table: str,
 ) -> bool:
    if not _table_exists(table_name):
        return False
    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
        if (
            foreign_key.get("constrained_columns") == constrained_columns
            and foreign_key.get("referred_table") == referred_table
        ):
            return True
    return False
 def _foreign_key_names_for_column(table_name: str, column_name: str) -> list[str]:
    if not _table_exists(table_name):
        return []
    names: list[str] = []
    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
        if column_name in foreign_key.get("constrained_columns", []):
            name = foreign_key.get("name")
            if name:
                names.append(name)
    return names
 def upgrade() -> None:
    if not _column_exists("config_profiles", "project_id"):
        op.add_column(
            "config_profiles",
            sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
        )
    if not _column_exists("config_profiles", "tool_type_id"):
        op.add_column(
            "config_profiles",
            sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=True),
        )
    if not _column_exists("config_profiles", "environment_variables"):
        op.add_column(
            "config_profiles",
            sa.Column("environment_variables", sa.JSON(), nullable=True),
        )
    if not _column_exists("config_profiles", "start_command"):
        op.add_column(
            "config_profiles",
            sa.Column("start_command", sa.Text(), nullable=True),
        )
    if not _column_exists("config_profiles", "working_directory"):
        op.add_column(
            "config_profiles",
            sa.Column("working_directory", sa.Text(), nullable=True),
        )
    if not _column_exists("config_profiles", "port"):
        op.add_column("config_profiles", sa.Column("port", sa.Integer(), nullable=True))
    if not _column_exists("config_profiles", "is_default"):
        op.add_column(
            "config_profiles",
            sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
        )
    if not _foreign_key_exists("config_profiles", ["project_id"], "projects"):
        op.create_foreign_key(
            "fk_config_profiles_project",
            "config_profiles",
            "projects",
            ["project_id"],
            ["id"],
            ondelete="CASCADE",
        )
    if not _foreign_key_exists("config_profiles", ["tool_type_id"], "tool_types"):
        op.create_foreign_key(
            "fk_config_profiles_tool_type",
            "config_profiles",
            "tool_types",
            ["tool_type_id"],
            ["id"],
            ondelete="CASCADE",
        )
    if not _index_exists("config_profiles", "idx_config_profiles_project"):
        op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
    if not _index_exists("config_profiles", "idx_config_profiles_tool_type"):
        op.create_index(
            "idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"]
        )
    if _column_exists("config_mounts", "mount_path") and not _column_exists(
        "config_mounts", "target_path"
    ):
        op.alter_column("config_mounts", "mount_path", new_column_name="target_path")
    if not _column_exists("config_mounts", "mode"):
        op.add_column(
            "config_mounts",
            sa.Column("mode", sa.String(length=10), nullable=False, server_default="rw"),
        )
    if not _column_exists("config_mounts", "files"):
        op.add_column(
            "config_mounts",
            sa.Column("files", sa.JSON(), nullable=True),
        )
    for constraint_name in _foreign_key_names_for_column(
        "config_mounts", "source_profile_id"
    ):
        op.drop_constraint(constraint_name, "config_mounts", type_="foreignkey")
    if _column_exists("config_mounts", "content"):
        op.drop_column("config_mounts", "content")
    if _column_exists("config_mounts", "source_profile_id"):
        op.drop_column("config_mounts", "source_profile_id")
 def downgrade() -> None:
    # Restore config_mounts
    op.add_column(
        "config_mounts",
        sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
    )
    op.add_column(
        "config_mounts",
        sa.Column("content", sa.Text(), nullable=True),
    )
    op.drop_column("config_mounts", "files")
    op.drop_column("config_mounts", "mode")
    op.alter_column("config_mounts", "target_path", new_column_name="mount_path")
    # Restore config_profiles
    op.drop_index("idx_config_profiles_tool_type", table_name="config_profiles")
    op.drop_index("idx_config_profiles_project", table_name="config_profiles")
    op.drop_constraint(
        "fk_config_profiles_tool_type", "config_profiles", type_="foreignkey"
    )
    op.drop_constraint("fk_config_profiles_project", "config_profiles", type_="foreignkey")
    op.drop_column("config_profiles", "is_default")
    op.drop_column("config_profiles", "port")
    op.drop_column("config_profiles", "working_directory")
    op.drop_column("config_profiles", "start_command")
    op.drop_column("config_profiles", "environment_variables")
    op.drop_column("config_profiles", "tool_type_id")
    op.drop_column("config_profiles", "project_id")
@@ -104,11 +104,11 @@ RUN git config --global init.defaultBranch main \\
    && git config --global user.name "Developer"
 # Create default tmux config
-RUN printf '%s\\n' 'set -g mouse on' 'set -g default-terminal "screen-256color"' > /home/user/.tmux.conf
+RUN echo 'set -g mouse on\\nset -g default-terminal "screen-256color"' > /home/user/.tmux.conf
 # Create default ranger config
 RUN mkdir -p /home/user/.config/ranger \\
-    && printf '%s\\n' 'set preview_files true' 'set use_preview_script true' > /home/user/.config/ranger/rc.conf
+    && echo 'set preview_files true\\nset use_preview_script true' > /home/user/.config/ranger/rc.conf
 # Set up Pi config directory
 RUN mkdir -p /home/user/.pi/agent
@@ -232,6 +232,20 @@ 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"],
@@ -308,10 +322,10 @@ RUN git config --global init.defaultBranch main \\
    && git config --global user.email "dev@headquarter.local" \\
    && git config --global user.name "Developer"
-RUN printf '%s\\n' 'set -g mouse on' 'set -g default-terminal "screen-256color"' > /home/user/.tmux.conf
+RUN echo 'set -g mouse on\\nset -g default-terminal "screen-256color"' > /home/user/.tmux.conf
 RUN mkdir -p /home/user/.config/ranger \\
-    && printf '%s\\n' 'set preview_files true' 'set use_preview_script true' > /home/user/.config/ranger/rc.conf
+    && echo 'set preview_files true\\nset use_preview_script true' > /home/user/.config/ranger/rc.conf
 RUN mkdir -p /home/user/.pi/agent
@@ -1,81 +0,0 @@
 """add workspaces table
 Revision ID: 2026_06_01_add_workspaces
 Revises: 2026_05_29_fix_code_server_bind_addr_port
 Create Date: 2026-06-01 10:00:00.000000
 """
 from collections.abc import Sequence
 from alembic import op
 import sqlalchemy as sa
 # revision identifiers, used by Alembic.
 revision: str = "2026_06_01_add_workspaces"
 down_revision: str | None = "2026_05_29_fix_code_server_bind_addr_port"
 branch_labels: str | Sequence[str] | None = None
 depends_on: str | Sequence[str] | None = None
 def upgrade() -> None:
    # Create workspaces table
    op.create_table(
        "workspaces",
        sa.Column("id", sa.Uuid(as_uuid=True), primary_key=True),
        sa.Column("name", sa.String(255), nullable=False),
        sa.Column(
            "repo_id",
            sa.Uuid(as_uuid=True),
            sa.ForeignKey("git_repositories.id", ondelete="CASCADE"),
            nullable=False,
        ),
        sa.Column(
            "user_id",
            sa.Uuid(as_uuid=True),
            sa.ForeignKey("users.id", ondelete="CASCADE"),
            nullable=False,
        ),
        sa.Column("branch", sa.String(255), nullable=False, server_default="main"),
        sa.Column("path", sa.String(2048), nullable=False),
        sa.Column("status", sa.String(16), nullable=False, server_default="ready"),
        sa.Column("last_sync_at", sa.DateTime(timezone=True), nullable=True),
        sa.Column(
            "created_at",
            sa.DateTime(timezone=True),
            server_default=sa.text("now()"),
            nullable=False,
        ),
        sa.Column(
            "updated_at",
            sa.DateTime(timezone=True),
            server_default=sa.text("now()"),
            nullable=False,
        ),
        sa.UniqueConstraint("repo_id", "name", name="uq_workspace_repo_name"),
        if_not_exists=True,
    )
    op.create_index("idx_workspaces_repo_id", "workspaces", ["repo_id"])
    op.create_index("idx_workspaces_user_id", "workspaces", ["user_id"])
    op.create_index("idx_workspaces_status", "workspaces", ["status"])
    # Add workspace_id to tool_instances
    op.add_column(
        "tool_instances",
        sa.Column(
            "workspace_id",
            sa.Uuid(as_uuid=True),
            sa.ForeignKey("workspaces.id", ondelete="SET NULL"),
            nullable=True,
        ),
    )
    op.create_index(
        "idx_tool_instances_workspace_id", "tool_instances", ["workspace_id"]
    )
 def downgrade() -> None:
    op.drop_index("idx_tool_instances_workspace_id", table_name="tool_instances")
    op.drop_column("tool_instances", "workspace_id")
    op.drop_table("workspaces")
@@ -1,35 +0,0 @@
 """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,
    )
@@ -1,89 +0,0 @@
 """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")
@@ -1,90 +0,0 @@
 """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)
@@ -1,86 +0,0 @@
 """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)
@@ -1,20 +0,0 @@
 """merge profile resolver and workspaces heads
 Revision ID: 86cec91fdb00
 Revises: 0014_add_profile_resolver_fields, 2026_06_01_add_workspaces
 Create Date: 2026-06-03 12:48:36.145702
 """
 # revision identifiers, used by Alembic.
 revision = "86cec91fdb00"
 down_revision = ("0014_add_profile_resolver_fields", "2026_06_01_add_workspaces")
 branch_labels = None
 depends_on = None
 def upgrade() -> None:
    pass
 def downgrade() -> None:
    pass
@@ -1,112 +0,0 @@
 """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,
        },
    )
@@ -1,23 +0,0 @@
 """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
@@ -1,54 +0,0 @@
 # apps/api/src (index)
 dir: apps/api/src
 ## role
 Core application package for the Headquarter API, handling configuration, database connectivity, logging infrastructure, and FastAPI application lifecycle.
 ## parent
 index: apps/api/.pi-map.index.md
 map: apps/api/.pi-map.md
 ## children
 - 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/api/.pi-map.index.md, apps/api/src/auth/.pi-map.index.md, apps/api/src/headquarter_api.egg-info/.pi-map.index.md
 ## dirty
 -
@@ -1,35 +0,0 @@
 # apps/api/src
 dir: apps/api/src
 index: apps/api/src/.pi-map.index.md
 ## role
 Core application package for the Headquarter API, handling configuration, database connectivity, logging infrastructure, and FastAPI application lifecycle.
 ## files
 - __init__.py | Marks the directory as a Python package for the Headquarter API.
 - config.py | Defines application configuration settings with environment-based overrides using Pydantic, including database URLs, service domains, OAuth/Authentik integration, JWT/session settings, and computed properties for environment-specific behavior. | exp: class:Settings, func:build_database_url(user: str, password: str, host: str, port: int, database: str) → str | dep: pydantic, pydantic_settings
 - database.py | Sets up async SQLAlchemy database engine and session factory, with retry logic for database connectivity testing and Alembic migration execution 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, custom formatters, and HTTP request/exception middleware for a FastAPI application. | 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
 - main.py | Initializes and configures a FastAPI application for the "Headquarter API" with database setup, middleware, routing, and background services. | 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.*
 ## arch
 Layered architecture with Pydantic-based settings management, async SQLAlchemy with Alembic migrations, structured JSON logging with correlation ID tracking, and modular FastAPI initialization with middleware pipeline.
 ## tags
 src, database, logging, call:logger.info, api, middleware, fastapi, filter
 ## 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/api/.pi-map.index.md, apps/api/src/auth/.pi-map.index.md, apps/api/src/headquarter_api.egg-info/.pi-map.index.md
 ## dirty
 -
@@ -1,40 +0,0 @@
 # apps/api/src/api (index)
 dir: apps/api/src/api
 ## role
 Defines the API routing package and shared validation utilities for the REST API layer.
 ## parent
 index: apps/api/src/.pi-map.index.md
 map: apps/api/src/.pi-map.md
 ## children
 - 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/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md, apps/api/src/api/system/.pi-map.index.md
 ## dirty
 -
@@ -1,30 +0,0 @@
 # apps/api/src/api
 dir: apps/api/src/api
 index: apps/api/src/api/.pi-map.index.md
 ## role
 Defines the API routing package and shared validation utilities for the REST API layer.
 ## files
 - __init__.py | Marks the directory as a Python package for API routers.
 - shared_validators.py | Provides reusable Pydantic validator functions for API schema validation including mount paths, files, environment variables, and volume mounts. | 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 with reusable Pydantic validators for cross-cutting API schema concerns.
 ## 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/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md, apps/api/src/api/system/.pi-map.index.md
 ## dirty
 -
@@ -1 +1,6 @@
-"""API routers package."""
+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"]
@@ -1,24 +0,0 @@
 # apps/api/src/api/config (index)
 dir: apps/api/src/api/config
 ## role
 Provides FastAPI API endpoints for managing user configuration settings and configuration 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
 -
@@ -1,31 +0,0 @@
 # 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 configuration profiles.
 ## files
 - __init__.py | Aggregates and exports configuration-related API routers for the config module. | dep: src.api.config.config_profiles, src.api.config.user_config
 - config_profiles.py | FastAPI router providing CRUD endpoints for user config profiles with includes, resolution, defaults, 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 to get and update the current user's configuration settings, creating a default config if none exists. | 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 FastAPI router pattern with separate route modules for distinct resource domains (user config vs config profiles), each implementing standard CRUD operations with validation and default initialization logic.
 ## tags
 config, profile, get, user, includes, call:uuid.uuid, 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
 -
@@ -1,6 +0,0 @@
 """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"]
@@ -1,300 +0,0 @@
 """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)
@@ -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 import GitRepository
+from src.models.git_repository import GitRepository
 from src.models.project import Project
-from src.models import SSHKey
+from src.models.ssh_key import SSHKey
 router = APIRouter(prefix="/dashboard", tags=["dashboard"])
@@ -10,13 +10,13 @@ from fastapi import APIRouter, Depends, HTTPException, Request, status
 from fastapi.responses import StreamingResponse
 from src.auth.dependencies import get_current_user_id
-from src.services.instance.event_bus import InstanceEventBus, InstanceEventPayload
+from src.services.event_bus import InstanceEventBus, InstanceEventPayload
 router = APIRouter(prefix="/events", tags=["events"])
 # In-memory connection counter per user (single-process assumption)
 _connection_counts: dict[uuid.UUID, int] = {}
-MAX_CONNECTIONS_PER_USER = 20
+MAX_CONNECTIONS_PER_USER = 5
@router.get("/stream")
@@ -5,16 +5,10 @@ from datetime import datetime, timezone
 from typing import Any
 from fastapi import APIRouter
 from pydantic import BaseModel, Field
 from sqlalchemy import text
 from src.database import SessionLocal
 from src.schemas.system import (
    DatabaseHealth,
    DatabaseHealthResponse,
    DiskHealth,
    HealthChecks,
    HealthResponse,
 )
 router = APIRouter()
@@ -22,6 +16,45 @@ router = APIRouter()
 _start_time = time.time()
 class DatabaseHealth(BaseModel):
    """Database health check result."""
    status: str = Field(description="Database health status", examples=["healthy"])
    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
 class DiskHealth(BaseModel):
    """Disk space health check result."""
    status: str = Field(description="Disk health status", examples=["healthy"])
    free_gb: float = Field(description="Free disk space in GB", examples=[45.2])
    total_gb: float = Field(description="Total disk space in GB", examples=[100.0])
 class HealthChecks(BaseModel):
    """Individual health checks."""
    database: DatabaseHealth | None = None
    disk: DiskHealth | None = None
 class HealthResponse(BaseModel):
    """Overall health check response."""
    status: str = Field(description="Overall health status", examples=["healthy"])
    timestamp: str = Field(description="ISO 8601 timestamp", examples=["2026-05-19T12:00:00Z"])
    version: str = Field(description="API version", examples=["0.1.0"])
    checks: HealthChecks = Field(description="Individual health checks")
    uptime_seconds: float = Field(description="Server uptime in seconds", examples=[3600.0])
 class DatabaseHealthResponse(BaseModel):
    """Database-specific health check response."""
    status: str = Field(description="Database health status", examples=["healthy"])
    response_time_ms: float = Field(description="Query response time in milliseconds", examples=[5.2])
@router.get(
    "/health",
    response_model=HealthResponse,
@@ -8,8 +8,8 @@ from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models import ToolInstance
+from src.models.tool_instance import ToolInstance
-from src.models import ToolType
+from src.models.tool_type 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 import UserConfig
+from src.models.user_config import UserConfig
-from src.services.shared.notification_service import notification_service
+from src.services.notification_service import notification_service
 router = APIRouter(prefix="/notifications", tags=["notifications"])
@@ -1,22 +0,0 @@
 # apps/api/src/api/project (index)
 dir: apps/api/src/api/project
 ## role
 Provides FastAPI REST API endpoints for project and Git repository management, serving as the HTTP interface layer for the project's core domain operations.
 ## 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
 -
@@ -1,6 +0,0 @@
 """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"]
@@ -1,500 +0,0 @@
 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))
@@ -3,29 +3,42 @@ import shutil
 import uuid
 from fastapi import APIRouter, Depends, HTTPException, Response, status
-from sqlalchemy import func, select
+from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
-from src.auth.dependencies import (
+from src.auth.dependencies import _get_owned_project, _get_user, get_current_user_id, get_db_session
-    _get_owned_project,
+from src.models.git_repository import GitRepository
    _get_user,
    get_current_user_id,
    get_db_session,
 )
 from src.models import GitRepository
 from src.models.project import Project
-from src.models import SSHKey
+from src.models.ssh_key import SSHKey
 from src.models import ToolInstance
 from src.schemas.project import (
    ProjectCreate,
    ProjectResponse,
    ProjectUpdate,
    SetDefaultSSHKeyRequest,
 )
 router = APIRouter(prefix="/projects", tags=["projects"])
 class ProjectCreate(BaseModel):
    name: str
    description: str | None = None
 class ProjectUpdate(BaseModel):
    name: str | None = None
    description: str | None = None
 class ProjectResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)
    id: uuid.UUID
    name: str
    description: str | None
    owner_id: uuid.UUID
    default_ssh_key_id: uuid.UUID | None
 class SetDefaultSSHKeyRequest(BaseModel):
    ssh_key_id: uuid.UUID
@router.post(
    "",
    response_model=ProjectResponse,
@@ -63,77 +76,26 @@ async def create_project(
@router.get(
    "",
    response_model=list[ProjectResponse],
    summary="List all projects",
-    description="Retrieve all projects owned by the authenticated user with repositories and workspaces.",
+    description="Retrieve all projects owned by the authenticated user.",
 )
 async def list_projects(
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
-) -> list[dict]:
+) -> list[Project]:
    """List all projects for the authenticated user.
-    Returns projects with nested repositories and workspaces for inline display.
+    Args:
        user_id: ID of the authenticated user.
        session: Database session.
    Returns:
        List of projects owned by the user.
    """
    user = await _get_user(session, user_id)
-    result = await session.execute(
+    result = await session.execute(select(Project).where(Project.owner_id == user.id))
-        select(Project)
+    return list(result.scalars().all())
        .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(
@@ -222,9 +184,7 @@ async def delete_project(
    project = await _get_owned_project(project_id, user_id, session)
    # Delete repositories from disk and database
-    result = await session.execute(
+    result = await session.execute(select(GitRepository).where(GitRepository.project_id == project_id))
        select(GitRepository).where(GitRepository.project_id == project_id)
    )
    repositories = result.scalars().all()
    for repo in repositories:
        if os.path.exists(repo.path):
@@ -1,24 +1,18 @@
 import base64
 import uuid
 from datetime import datetime
 from cryptography.fernet import Fernet
 from cryptography.hazmat.primitives import serialization
 from cryptography.hazmat.primitives.asymmetric.ed25519 import Ed25519PrivateKey
 from fastapi import APIRouter, Depends, HTTPException, status
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.config import Settings
-from src.models import SSHKey
+from src.models.ssh_key import SSHKey
 from src.schemas.project import (
    SSHKeyCreate,
    SSHKeyResponse,
    SignPayloadRequest,
    SignatureResponse,
    VerifySignatureRequest,
    VerifySignatureResponse,
 )
 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
@@ -27,7 +21,7 @@ def _get_fernet() -> Fernet:
    """Generate a valid Fernet key from the session secret."""
    import base64
    import hashlib
-
+    
    settings = Settings()
    # Derive a 32-byte key from the session secret using SHA256
    key_bytes = hashlib.sha256(settings.session_secret.encode()).digest()
@@ -59,6 +53,36 @@ def generate_ssh_key_pair() -> tuple[str, str]:
    return private_bytes.decode("utf-8"), public_bytes.decode("utf-8")
 class SSHKeyCreate(BaseModel):
    name: str
 class SSHKeyResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)
    id: uuid.UUID
    name: str
    public_key: str
    created_at: datetime
 class SignPayloadRequest(BaseModel):
    payload: str
 class SignatureResponse(BaseModel):
    signature: str
 class VerifySignatureRequest(BaseModel):
    payload: str
    signature: str
 class VerifySignatureResponse(BaseModel):
    valid: bool
@router.post(
    "",
    response_model=SSHKeyResponse,
@@ -147,9 +171,7 @@ async def delete_ssh_key(
    user = await _get_user(session, user_id)
    ssh_key = await session.get(SSHKey, key_id)
    if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
        )
    await session.delete(ssh_key)
    await session.commit()
@@ -181,9 +203,7 @@ async def sign_payload(
    user = await _get_user(session, user_id)
    ssh_key = await session.get(SSHKey, key_id)
    if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
            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()
@@ -222,9 +242,7 @@ async def verify_signature(
    user = await _get_user(session, user_id)
    ssh_key = await session.get(SSHKey, key_id)
    if ssh_key is None or ssh_key.user_id != user.id:
-        raise HTTPException(
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found")
            status_code=status.HTTP_404_NOT_FOUND, detail="ssh key not found"
        )
    public_key = serialization.load_ssh_public_key(ssh_key.public_key.encode())
@@ -1,26 +0,0 @@
 # apps/api/src/api/system (index)
 dir: apps/api/src/api/system
 ## role
 Provides system-level API endpoints for monitoring, administration, and infrastructure interaction including dashboards, health checks, event streaming, notifications, and container terminal access.
 ## parent
 index: apps/api/src/api/.pi-map.index.md
 map: apps/api/src/api/.pi-map.md
 ## children
 -
 ## 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
 ## dirty
 -
@@ -1,33 +0,0 @@
 # 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 interaction including dashboards, health checks, event streaming, notifications, and container terminal access.
 ## files
 - __init__.py | Aggregates and re-exports system API router modules from submodules for centralized access. | 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 aggregated 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, src.models (GitRepository, Project, SSHKey)
 - events.py | Implements an SSE streaming endpoint that delivers instance events to authenticated users with per-user connection limits and keep-alive pings. | exp: func:events_stream(request: Request, user_id) → StreamingResponse, call:_connection_counts.get, call:InstanceEventBus, call:asyncio.Queue, call:queue.put_nowait, call:contextlib.suppress, call:queue.get_nowait, call:event_bus.subscribe, call:asyncio.wait_for, call:queue.get, call:json.dumps, call:unsubscribe, call:max, call:_connection_counts.pop, call:StreamingResponse, call:event_generator, raise:HTTPException, func:event_generator() → AsyncGenerator[str, None], call:InstanceEventBus, call:asyncio.Queue, call:queue.put_nowait, call:contextlib.suppress, call:queue.get_nowait, call:event_bus.subscribe, call:asyncio.wait_for, call:queue.get, call:json.dumps, call:unsubscribe, call:max, call:_connection_counts.get, call:_connection_counts.pop, func:on_event(payload: InstanceEventPayload) → None, call:queue.put_nowait, call:contextlib.suppress, call:queue.get_nowait | dep: asyncio, contextlib, json, uuid, collections.abc, fastapi, fastapi.responses, src.auth.dependencies, src.services.instance.event_bus
 - health.py | Implements FastAPI health check endpoints for monitoring system status including database connectivity and disk space. | 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 FastAPI endpoints to running containerized tool instances after verifying ownership and 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 managing user notifications (list, unread count, mark read, dismiss/clear) with support for muted categories from user config. | 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 and HTTP endpoints for managing interactive terminal sessions attached to running Docker container tool instances, including session creation, attachment, input/output streaming, resize/reset control messages, and session listing. | 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:_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: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: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: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: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.terminal.terminal_manager, src.services.docker, src.auth.session, src.config, starlette
 ## arch
 FastAPI router modules organized by domain concern with async/await patterns, SSE/WebSocket for real-time streaming, proxy pattern for container instance forwarding, and per-user authentication/authorization with connection limiting.
 ## tags
 session, terminal, call:terminal, call:, src, get, response, websocket
 ## symbols
 - NotificationItem
 - NotificationListResponse
 - UnreadCountResponse
 - MarkAllReadResponse
 - ClearAllResponse
 - SessionRef
 - get_dashboard_summary
 - events_stream
 ## workflows
 - change system behavior
  read: __init__.py, dashboard.py, events.py
 ## dirty
 -
@@ -1,17 +0,0 @@
 """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",
 ]
@@ -12,10 +12,10 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from starlette.websockets import WebSocketDisconnect
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models import TerminalSessionModel
+from src.models.terminal_session import TerminalSessionModel
-from src.models import ToolInstance
+from src.models.tool_instance import ToolInstance
-from src.models import ToolType
+from src.models.tool_type import ToolType
-from src.services.terminal.terminal_manager import MaxSessionsExceededError, terminal_manager
+from src.services.terminal_manager import MaxSessionsExceededError, terminal_manager
 router = APIRouter()
 logger = logging.getLogger(__name__)
@@ -222,7 +222,8 @@ async def _handle_terminal_websocket(
        # Use mutable session reference so loops can survive reset
        session_ref = SessionRef(session, slot_session_id)
-        # Start write loop and heartbeat (read is now event-driven in TerminalSession)
+        # Start I/O loops and heartbeat
        read_task = asyncio.create_task(_read_loop(session_ref, websocket))
        write_task = asyncio.create_task(
            _write_loop(session_ref, websocket, instance_id)
        )
@@ -231,7 +232,7 @@ async def _handle_terminal_websocket(
        # Wait for either task to complete (indicating disconnect or error)
        done, pending = await asyncio.wait(
-            [write_task, heartbeat_task],
+            [read_task, write_task, heartbeat_task],
            return_when=asyncio.FIRST_COMPLETED,
        )
@@ -266,6 +267,28 @@ async def _handle_terminal_websocket(
                )
 async def _read_loop(session_ref: SessionRef, websocket) -> None:
    """Read output from the container and send to WebSocket."""
    try:
        while True:
            session = session_ref.session
            if not session.is_alive() or session._closed:
                await asyncio.sleep(0.1)
                continue
            data = await session.read_output()
            if data:
                try:
                    await websocket.send_bytes(data)
                except WebSocketDisconnect:
                    break
                except Exception:
                    break
            else:
                await asyncio.sleep(0.01)
    except Exception:
        pass
 async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> None:
    """Read input from WebSocket and send to container."""
    try:
@@ -296,10 +319,6 @@ async def _write_loop(session_ref: SessionRef, websocket, instance_id: str) -> N
                                    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(
@@ -1,26 +0,0 @@
 # apps/api/src/api/tool (index)
 dir: apps/api/src/api/tool
 ## role
 Provides FastAPI REST API endpoints for managing Docker-based tools, including their definitions, types, instances, lifecycle operations, and active sessions.
 ## 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
 -
@@ -1,33 +0,0 @@
 # 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 Docker-based tools, including their definitions, types, instances, lifecycle operations, and active sessions.
 ## files
 - __init__.py | Aggregates and exports all tool-related API routers from submodules as a unified module interface. | 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 instances (sessions) 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, src.models (GitRepository, Project, ToolInstance, ToolType, Workspace)
 - tool_definitions.py | FastAPI router providing CRUD endpoints and manifest compilation for tool definition manifests stored in a database. | 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 | Provides FastAPI REST endpoints for managing tool instances including CRUD operations, logs, health checks, tunnel recreation, event history, and HTTP proxying to running containers. | 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 routes for CRUD operations and validation of Docker tool types with compose/dockerfile/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 | Validates Docker Compose YAML templates by sanitizing template variables, parsing YAML structure, checking port exposure, and verifying required variables exist. | 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 organization with clear separation of concerns across CRUD operations, Docker lifecycle management, YAML/Compose validation, and container proxying/tunneling.
 ## 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
 -
@@ -1,15 +0,0 @@
 """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",
 ]
@@ -1,86 +0,0 @@
 """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}
@@ -1,419 +0,0 @@
 """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,
    )
@@ -1,135 +0,0 @@
 """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
        )
@@ -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 import ToolDefinitionManifest
+from src.models.tool_definition_manifest import ToolDefinitionManifest
-from src.models import ToolType
+from src.models.tool_type import ToolType
-from src.services.build.manifest_compiler import (
+from src.services.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.is_(False))
+        query = query.where(ToolDefinitionManifest.is_base == False)
    result = await session.execute(
        query.order_by(ToolDefinitionManifest.created_at.desc())
@@ -1,23 +1,19 @@
 import uuid
 from datetime import datetime
 from fastapi import APIRouter, Depends, HTTPException, status
 from pydantic import BaseModel, ConfigDict, field_validator, model_validator
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
-from src.api.tool.tool_types_validation import (
+from src.api.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.tool_type import ToolType
 from src.models.user import User
 from src.schemas.tool import (
    ToolTypeCreate,
    ToolTypeResponse,
    ToolTypeUpdate,
    ToolTypeValidateRequest,
 )
 router = APIRouter(prefix="/tool-types", tags=["tool-types"])
@@ -33,6 +29,237 @@ async def _require_admin(user: User) -> None:
    pass
 class ToolTypeCreate(BaseModel):
    name: str
    display_name: str
    description: str | None = None
    default_port: int = 0
    definition_type: str = "compose"
    manifest_id: uuid.UUID | None = None
    compose_template: str | None = None
    dockerfile_template: str | None = None
    build_context: dict | None = None
    readiness_probe: dict | None = None
    startup_command: str | None = None
    required_variables: list[str] = []
    category: str = "other"
    interface_type: str = "web"
    requires_port: bool = True
    @field_validator("definition_type")
    @classmethod
    def validate_definition_type(cls, v: str) -> str:
        if v not in ("compose", "dockerfile", "manifest"):
            raise ValueError(
                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
            )
        return v
    @field_validator("compose_template")
    @classmethod
    def validate_compose_template(cls, v: str | None, info) -> str | None:
        data = info.data
        if data.get("definition_type") != "compose":
            return v
        if v is None or not v.strip():
            raise ValueError(
                "compose_template is required when definition_type is 'compose'"
            )
        validate_compose_yaml(v)
        return v
    @field_validator("dockerfile_template")
    @classmethod
    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
        data = info.data
        if data.get("definition_type") != "dockerfile":
            return v
        if v is None or not v.strip():
            raise ValueError(
                "dockerfile_template is required when definition_type is 'dockerfile'"
            )
        if not v.strip().startswith("FROM"):
            raise ValueError("Dockerfile must start with a FROM instruction")
        return v
    @field_validator("interface_type")
    @classmethod
    def validate_interface_type(cls, v: str) -> str:
        if v not in ("web", "terminal"):
            raise ValueError("interface_type must be 'web' or 'terminal'")
        return v
    @field_validator("default_port")
    @classmethod
    def validate_default_port(cls, v: int, info) -> int:
        data = info.data
        requires_port = data.get("requires_port", True)
        if not requires_port:
            return v
        if v <= 0 or v > 65535:
            raise ValueError("Port must be between 1 and 65535")
        return v
    @field_validator("required_variables")
    @classmethod
    def validate_required_variables(cls, v: list[str], info) -> list[str]:
        if not v:
            return v
        data = info.data
        if data.get("definition_type") != "compose":
            return v
        template = data.get("compose_template")
        if not template:
            return v
        for var in v:
            placeholder = f"{{{{{var}}}}}"
            if placeholder not in template:
                raise ValueError(
                    f"Required variable '{var}' not found in compose template"
                )
        return v
    @model_validator(mode="after")
    def validate_templates(self) -> "ToolTypeCreate":
        if self.definition_type == "manifest":
            if self.manifest_id is None:
                raise ValueError(
                    "manifest_id is required when definition_type is 'manifest'"
                )
            return self
        if self.definition_type == "dockerfile" and (
            self.dockerfile_template is None or not self.dockerfile_template.strip()
        ):
            raise ValueError(
                "dockerfile_template is required when definition_type is 'dockerfile'"
            )
        if self.definition_type == "compose" and (
            self.compose_template is None or not self.compose_template.strip()
        ):
            raise ValueError(
                "compose_template is required when definition_type is 'compose'"
            )
        # Validate that default_port is exposed in compose template (only if requires_port)
        if (
            self.requires_port
            and self.definition_type == "compose"
            and self.compose_template
        ):
            try:
                parsed = validate_compose_yaml(self.compose_template)
            except ValueError:
                return self
            if not check_port_exposed(parsed, self.default_port):
                raise ValueError(
                    f"Port {self.default_port} is not exposed in the compose template. Add it to the 'ports' section."
                )
        return self
 class ToolTypeUpdate(BaseModel):
    display_name: str | None = None
    description: str | None = None
    default_port: int | None = None
    definition_type: str | None = None
    manifest_id: uuid.UUID | None = None
    compose_template: str | None = None
    dockerfile_template: str | None = None
    build_context: dict | None = None
    readiness_probe: dict | None = None
    startup_command: str | None = None
    required_variables: list[str] | None = None
    category: str | None = None
    interface_type: str | None = None
    requires_port: bool | None = None
    @field_validator("definition_type")
    @classmethod
    def validate_definition_type(cls, v: str | None) -> str | None:
        if v is None:
            return v
        if v not in ("compose", "dockerfile", "manifest"):
            raise ValueError(
                "definition_type must be 'compose', 'dockerfile', or 'manifest'"
            )
        return v
    @field_validator("interface_type")
    @classmethod
    def validate_interface_type(cls, v: str | None) -> str | None:
        if v is None:
            return v
        if v not in ("web", "terminal"):
            raise ValueError("interface_type must be 'web' or 'terminal'")
        return v
    @field_validator("compose_template")
    @classmethod
    def validate_compose_template(cls, v: str | None, info) -> str | None:
        if v is None:
            return v
        data = info.data
        definition_type = data.get("definition_type")
        if definition_type and definition_type != "compose":
            return v
        validate_compose_yaml(v)
        return v
    @field_validator("dockerfile_template")
    @classmethod
    def validate_dockerfile_template(cls, v: str | None, info) -> str | None:
        if v is None:
            return v
        data = info.data
        definition_type = data.get("definition_type")
        if definition_type and definition_type != "dockerfile":
            return v
        if not v.strip().startswith("FROM"):
            raise ValueError("Dockerfile must start with a FROM instruction")
        return v
 class ToolTypeResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)
    id: uuid.UUID
    name: str
    display_name: str
    description: str | None
    category: str
    interface_type: str
    requires_port: bool
    default_port: int
    definition_type: str
    manifest_id: uuid.UUID | None
    compose_template: str | None
    dockerfile_template: str | None
    build_context: dict | None
    readiness_probe: dict | None
    startup_command: str | None
    required_variables: list[str]
    created_by_id: uuid.UUID | None
    created_at: datetime
    updated_at: datetime
@router.post(
    "",
    response_model=ToolTypeResponse,
@@ -234,6 +461,12 @@ async def update_tool_type(
    return tool_type
 class ToolTypeValidateRequest(BaseModel):
    definition_type: str
    compose_template: str | None = None
    dockerfile_template: str | None = None
@router.post(
    "/validate",
    summary="Validate tool type template",
@@ -60,14 +60,8 @@ 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):
+                if isinstance(port_mapping, str) and port_str in port_mapping:
-                    # Port mappings can be "host:container", "ip:host:container",
+                    return True
                    # "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
@@ -1,23 +0,0 @@
 # apps/api/src/api/user (index)
 dir: apps/api/src/api/user
 ## role
 Provides authentication, user profile management, and SSH key operations for the API 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
 -
@@ -1,30 +0,0 @@
 # apps/api/src/api/user
 dir: apps/api/src/api/user
 index: apps/api/src/api/user/.pi-map.index.md
 ## role
 Provides authentication, user profile management, and SSH key operations for the API 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, 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 | Implements a FastAPI router for managing Ed25519 SSH key pairs, including generation, storage with encrypted private keys, listing, deletion, and cryptographic signing/verification operations. | 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 authenticated user profile management including retrieval, updates, and avatar uploads. | 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
 ## arch
 Modular FastAPI router pattern with OAuth2/OIDC external identity provider integration, encrypted key storage, and file-based avatar 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
 -
@@ -1,7 +0,0 @@
 """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"]
@@ -2,12 +2,12 @@ import logging
 import uuid
 from fastapi import APIRouter, Depends
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
-from src.models import UserConfig
+from src.models.user_config import UserConfig
 from src.schemas.user import UserConfigResponse, UserConfigUpdate
 logger = logging.getLogger(__name__)
@@ -38,6 +38,28 @@ async def _get_or_create_config(
    return config
 class UserConfigResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)
    default_editor: str | None = None
    theme: str = "system"
    git_user_name: str | None = None
    git_user_email: str | None = None
    last_session_id: str | None = None
    notification_mute_categories: list[str] | None = None
    notification_toast_level: str | None = None
 class UserConfigUpdate(BaseModel):
    default_editor: str | None = None
    theme: str | None = None
    git_user_name: str | None = None
    git_user_email: str | None = None
    last_session_id: str | None = None
    notification_mute_categories: list[str] | None = None
    notification_toast_level: str | None = None
@router.get(
    "/config",
    response_model=UserConfigResponse,
@@ -2,11 +2,11 @@ import uuid
 from pathlib import Path
 from fastapi import APIRouter, Depends, HTTPException, UploadFile, status
 from pydantic import BaseModel, ConfigDict
 from sqlalchemy.ext.asyncio import AsyncSession
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.models.user import User
 from src.schemas.user import UserProfileResponse, UserProfileUpdate
 router = APIRouter(prefix="/users", tags=["users"])
@@ -16,6 +16,20 @@ ALLOWED_CONTENT_TYPES = {"image/png", "image/jpeg", "image/jpg"}
 MAX_AVATAR_SIZE = 2 * 1024 * 1024  # 2MB
 class UserProfileResponse(BaseModel):
    model_config = ConfigDict(from_attributes=True)
    id: uuid.UUID
    email: str
    name: str
    avatar_url: str | None
 class UserProfileUpdate(BaseModel):
    name: str | None = None
    email: str | None = None
@router.get(
    "/me",
    response_model=UserProfileResponse,
@@ -63,16 +77,12 @@ async def update_profile(
    if data.name is not None:
        if len(data.name.strip()) == 0:
-            raise HTTPException(
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="name cannot be empty")
                status_code=status.HTTP_400_BAD_REQUEST, detail="name cannot be empty"
            )
        user.name = data.name.strip()
    if data.email is not None:
        if "@" not in data.email:
-            raise HTTPException(
+            raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="invalid email")
                status_code=status.HTTP_400_BAD_REQUEST, detail="invalid email"
            )
        user.email = data.email.strip()
    await session.commit()
@@ -1,24 +0,0 @@
 # apps/api/src/api/workspace (index)
 dir: apps/api/src/api/workspace
 ## role
 Provides FastAPI REST API endpoints for workspace management, including file operations, git version control, and tool instance orchestration within user-scoped development environments.
 ## 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
 -
@@ -1,31 +0,0 @@
 # apps/api/src/api/workspace
 dir: apps/api/src/api/workspace
 index: apps/api/src/api/workspace/.pi-map.index.md
 ## role
 Provides FastAPI REST API endpoints for workspace management, including file operations, git version control, and tool instance orchestration within user-scoped development environments.
 ## files
 - __init__.py | Aggregates and re-exports workspace API router modules 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 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 git operations (status, branches, commit, push, pull, fetch, checkout, history) scoped to user workspaces. | 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 | FastAPI router providing endpoints to create and list 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 repository workspaces with nested and top-level URL structures. | 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 router-based FastAPI architecture with domain-driven separation of concerns (files, git, instances, workspaces) using nested URL routing patterns and explicit dependency injection for cross-cutting workspace context.
 ## 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
 -
@@ -1,17 +0,0 @@
 """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",
 ]
@@ -1,114 +0,0 @@
 """Workspace file API endpoints."""
 import uuid
 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 import Workspace
 from src.services.shared.file_service import FileService
 router = APIRouter(prefix="/workspaces/{workspace_id}/files")
 async def _get_workspace(
    session: AsyncSession,
    workspace_id: uuid.UUID,
    user_id: uuid.UUID,
 ) -> Workspace:
    from sqlalchemy import select
    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_files(
    workspace_id: uuid.UUID,
    path: str = "",
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """List files in a workspace directory."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    service = FileService()
    try:
        entries = service.list_directory(workspace, path)
    except ValueError as exc:
        raise HTTPException(status_code=400, detail=str(exc)) from exc
    return {
        "entries": [
            {
                "name": e.name,
                "path": e.path,
                "type": e.type,
                "size": e.size,
            }
            for e in entries
        ],
    }
@router.get("/content")
 async def get_file_content(
    workspace_id: uuid.UUID,
    path: str,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Get the content of a text file."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    service = FileService()
    try:
        content = service.read_file(workspace, path)
    except FileNotFoundError as exc:
        raise HTTPException(status_code=404, detail=str(exc)) from exc
    except ValueError as exc:
        raise HTTPException(status_code=400, detail=str(exc)) from exc
    return {"content": content, "path": path}
@router.post("/content")
 async def write_file(
    workspace_id: uuid.UUID,
    data: dict,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Write a file and optionally commit."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    service = FileService()
    file_path = data.get("path", "").strip()
    content = data.get("content", "")
    commit_message = data.get("message", "").strip()
    if not file_path:
        raise HTTPException(status_code=400, detail="File path is required")
    try:
        service.write_file(workspace, file_path, content)
    except ValueError as exc:
        raise HTTPException(status_code=400, detail=str(exc)) from exc
    if commit_message:
        from src.services.git.git_operations import GitOperations
        git = GitOperations(workspace)
        try:
            await git.commit(commit_message)
        except RuntimeError as exc:
            raise HTTPException(status_code=500, detail=str(exc)) from exc
    return {"status": "saved", "path": file_path}
@@ -1,203 +0,0 @@
 """Workspace git API endpoints."""
 import uuid
 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 import Workspace
 from src.services.git.git_operations import GitOperations
 router = APIRouter(prefix="/workspaces/{workspace_id}/git")
 async def _get_workspace(
    session: AsyncSession,
    workspace_id: uuid.UUID,
    user_id: uuid.UUID,
 ) -> Workspace:
    from sqlalchemy import select
    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("/status")
 async def git_status(
    workspace_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Get git status for the workspace."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    git = GitOperations(workspace)
    try:
        status = await git.status()
    except RuntimeError as exc:
        raise HTTPException(status_code=500, detail=str(exc)) from exc
    return {
        "branch": status.branch,
        "modified": status.modified,
        "added": status.added,
        "deleted": status.deleted,
        "untracked": status.untracked,
        "ahead": status.ahead,
        "behind": status.behind,
    }
@router.get("/branches")
 async def git_branches(
    workspace_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """List branches for the workspace."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    git = GitOperations(workspace)
    try:
        branches, current = await git.branches()
    except RuntimeError as exc:
        raise HTTPException(status_code=500, detail=str(exc)) from exc
    return {
        "branches": branches,
        "current_branch": current,
    }
@router.post("/commit")
 async def git_commit(
    workspace_id: uuid.UUID,
    data: dict,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Stage all changes and commit."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    message = data.get("message", "").strip()
    if not message:
        raise HTTPException(status_code=400, detail="Commit message is required")
    git = GitOperations(workspace)
    try:
        await git.commit(message)
    except RuntimeError as exc:
        raise HTTPException(status_code=500, detail=str(exc)) from exc
    return {"status": "committed"}
@router.post("/push")
 async def git_push(
    workspace_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Push current branch."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    git = GitOperations(workspace)
    try:
        await git.push()
    except RuntimeError as exc:
        raise HTTPException(status_code=500, detail=str(exc)) from exc
    return {"status": "pushed"}
@router.post("/pull")
 async def git_pull(
    workspace_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Pull current branch."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    git = GitOperations(workspace)
    try:
        await git.pull()
    except RuntimeError as exc:
        raise HTTPException(status_code=500, detail=str(exc)) from exc
    return {"status": "pulled"}
@router.post("/fetch")
 async def git_fetch(
    workspace_id: uuid.UUID,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Fetch from origin."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    git = GitOperations(workspace)
    try:
        await git.fetch()
    except RuntimeError as exc:
        raise HTTPException(status_code=500, detail=str(exc)) from exc
    return {"status": "fetched"}
@router.post("/checkout")
 async def git_checkout(
    workspace_id: uuid.UUID,
    data: dict,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Checkout a branch."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    branch = data.get("branch", "").strip()
    if not branch:
        raise HTTPException(status_code=400, detail="Branch name is required")
    git = GitOperations(workspace)
    try:
        await git.checkout(branch)
    except RuntimeError as exc:
        raise HTTPException(status_code=500, detail=str(exc)) from exc
    workspace.branch = branch
    await session.commit()
    return {"status": "checked_out", "branch": branch}
@router.get("/history")
 async def git_history(
    workspace_id: uuid.UUID,
    path: str | None = None,
    limit: int = 50,
    user_id: uuid.UUID = Depends(get_current_user_id),
    session: AsyncSession = Depends(get_db_session),
 ) -> dict:
    """Get commit history."""
    workspace = await _get_workspace(session, workspace_id, user_id)
    git = GitOperations(workspace)
    try:
        commits = await git.history(path, limit)
    except RuntimeError as exc:
        raise HTTPException(status_code=500, detail=str(exc)) from exc
    return {
        "commits": [
            {
                "hash": c.hash,
                "message": c.message,
                "author": c.author,
                "date": c.date,
            }
            for c in commits
        ],
    }
@@ -1,120 +0,0 @@
 """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
    ]
--- a/Show More
+++ b/Show More