chore: merge project map patches

chore: patch project maps after workspace detail formatting
Regenerate .pi-map*.md files for files touched by the formatting pass.
2026-06-12 19:09:15 +00:00 · 2026-06-12 19:09:15 +00:00 · 2026-06-12 19:08:16 +00:00 · 2026-06-12 19:08:16 +00:00 · 2026-06-12 18:53:23 +00:00 · 2026-06-12 18:53:23 +00:00
846 changed files with 33568 additions and 19313 deletions
@@ -1,3 +1,3 @@
 {
-  "fingerprint": "c36b11ec5edebc02aa51b1113a7a11dc2559e812"
+  "fingerprint": "639c16d45210921c3c8ece071ef18bbe0c426ea2"
 }
@@ -1,14 +1,13 @@
-# Skill Registry — headquarter
+# Skill Registry — workspace

 <!-- Auto-generated by gentle-pi extensions/skill-registry.ts. Run /skill-registry:refresh to regenerate. -->

-Last updated: 2026-06-02
+Last updated: 2026-06-05

 ## Sources scanned

 - .opencode/skills
 - .claude/skills
- /home/alex/.config/opencode/skills

 ## Contract

@@ -20,12 +19,11 @@ Last updated: 2026-06-02

 | Skill | Trigger / description | Scope | Path |
 | --- | --- | --- | --- |
-| `auto-commit` | Use when you are making multiple edits or completing significant work in a git repository to automatically create commits | user | `/home/alex/.config/opencode/skills/auto-commit/SKILL.md` |
-| `openspec-apply-change` | Implement tasks from an OpenSpec change. Use when the user wants to start implementing, continue implementation, or work through tasks. | project | `/home/alex/projects/headquarter/.opencode/skills/openspec-apply-change/SKILL.md` |
-| `openspec-archive-change` | Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete. | project | `/home/alex/projects/headquarter/.opencode/skills/openspec-archive-change/SKILL.md` |
-| `openspec-explore` | Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change. | project | `/home/alex/projects/headquarter/.opencode/skills/openspec-explore/SKILL.md` |
-| `openspec-propose` | Propose a new change with all artifacts generated in one step. Use when the user wants to quickly describe what they want to build and get a complete proposal with design, specs, and tasks ready for implementation. | project | `/home/alex/projects/headquarter/.opencode/skills/openspec-propose/SKILL.md` |
-| `sift-backlog` | Triage and organize backlog tasks into actionable plans. Use when asked to review the backlog, prioritize tasks, create plans from backlog items, or move tasks from backlog to open status. Handles the full workflow of listing backlog tasks, grouping related tasks into plans, setting priorities and dependencies, activating plans, and changing task status from backlog to open. | project | `/home/alex/projects/headquarter/.claude/skills/sift-backlog/SKILL.md` |
+| `openspec-apply-change` | Implement tasks from an OpenSpec change. Use when the user wants to start implementing, continue implementation, or work through tasks. | project | `/workspace/.opencode/skills/openspec-apply-change/SKILL.md` |
+| `openspec-archive-change` | Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete. | project | `/workspace/.opencode/skills/openspec-archive-change/SKILL.md` |
+| `openspec-explore` | Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change. | project | `/workspace/.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 | `/workspace/.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 | `/workspace/.claude/skills/sift-backlog/SKILL.md` |

 ## Loading protocol

@@ -0,0 +1,20 @@
+# .claude (index)
+dir: .claude
+
+## role
+Configuration and instruction files for the Claude AI assistant integration.
+## parent
+index: ./.pi-map.index.md
+map: ./.pi-map.md
+## children
+- .claude/skills
+  index: .claude/skills/.pi-map.index.md
+  map: .claude/skills/.pi-map.md
+## files
+## links
+index: .claude/.pi-map.index.md
+map: .claude/.pi-map.md
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,18 @@
+# .claude
+dir: .claude
+
+index: .claude/.pi-map.index.md
+
+## role
+Configuration and instruction files for the Claude AI assistant integration.
+## files
+## arch
+Simple flat-file configuration storage with no complex architecture; contains prompt templates, system instructions, or context files used to guide Claude's behavior in this project.
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,20 @@
+# .claude/skills (index)
+dir: .claude/skills
+
+## role
+Empty directory placeholder for future Claude Code skill definitions or custom AI-assisted workflows.
+## parent
+index: .claude/.pi-map.index.md
+map: .claude/.pi-map.md
+## children
+- .claude/skills/sift-backlog
+  index: .claude/skills/sift-backlog/.pi-map.index.md
+  map: .claude/skills/sift-backlog/.pi-map.md
+## files
+## links
+index: .claude/skills/.pi-map.index.md
+map: .claude/skills/.pi-map.md
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,18 @@
+# .claude/skills
+dir: .claude/skills
+
+index: .claude/skills/.pi-map.index.md
+
+## role
+Empty directory placeholder for future Claude Code skill definitions or custom AI-assisted workflows.
+## files
+## arch
+None (no files present); likely intended for declarative skill modules using Claude's skill system pattern.
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,19 @@
+# .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
+-
@@ -0,0 +1,19 @@
+# .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
+Skill-based workflow automation following a structured triage pipeline (scan → filter → prioritize → activate) with CLI tool integration for backlog management.
+## tags
+skill, defines, workflow, triaging, organizing, activating, backlog, tasks
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -17,6 +17,7 @@ __pycache__/
 *.so
 .python-version
 .venv/
+.venv-test/
 venv/
 env/
 .pytest_cache/
@@ -54,3 +55,6 @@ Thumbs.db
 .atl/
 .sisyphus/
 .pi-lens/
+minerv3/
+.cache/
+openspec-audit-report.md
@@ -0,0 +1,23 @@
+# .opencode (index)
+dir: .opencode
+
+## role
+Configuration directory for the OpenCode AI coding assistant tool
+## parent
+index: ./.pi-map.index.md
+map: ./.pi-map.md
+## children
+- .opencode/commands
+  index: .opencode/commands/.pi-map.index.md
+  map: .opencode/commands/.pi-map.md
+- .opencode/skills
+  index: .opencode/skills/.pi-map.index.md
+  map: .opencode/skills/.pi-map.md
+## files
+## links
+index: .opencode/.pi-map.index.md
+map: .opencode/.pi-map.md
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,18 @@
+# .opencode
+dir: .opencode
+
+index: .opencode/.pi-map.index.md
+
+## role
+Configuration directory for the OpenCode AI coding assistant tool
+## files
+## arch
+Tool-specific configuration storage using standard dot-directory convention with likely JSON/YAML config files and optional workspace state/logs
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,22 @@
+# .opencode/commands (index)
+dir: .opencode/commands
+
+## role
+Defines structured workflow commands and AI assistant stances for an experimental OpenSpec-based development system that guides changes through exploration, proposal, implementation, and archival phases.
+## parent
+index: .opencode/.pi-map.index.md
+map: .opencode/.pi-map.md
+## children
+-
+## files
+- opsx-apply.md
+- opsx-archive.md
+- opsx-explore.md
+- opsx-propose.md
+## links
+index: .opencode/commands/.pi-map.index.md
+map: .opencode/commands/.pi-map.md
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,22 @@
+# .opencode/commands
+dir: .opencode/commands
+
+index: .opencode/commands/.pi-map.index.md
+
+## role
+Defines structured workflow commands and AI assistant stances for an experimental OpenSpec-based development system that guides changes through exploration, proposal, implementation, and archival phases.
+## 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 declarative workflow definitions using a command pattern where each `.md` file specifies a distinct operational stance or phase (explore/propose/apply/archive) with embedded metadata, structured steps, and CLI integration points for progressive change lifecycle management.
+## tags
+opsx, defines, workflow, openspec, openspec cli, askuserquestion tool, explore, experimental
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,29 @@
+# .opencode/skills (index)
+dir: .opencode/skills
+
+## role
+Contains reusable skill modules that provide specific capabilities or integrations for the OpenCode agent framework.
+## parent
+index: .opencode/.pi-map.index.md
+map: .opencode/.pi-map.md
+## children
+- .opencode/skills/openspec-apply-change
+  index: .opencode/skills/openspec-apply-change/.pi-map.index.md
+  map: .opencode/skills/openspec-apply-change/.pi-map.md
+- .opencode/skills/openspec-archive-change
+  index: .opencode/skills/openspec-archive-change/.pi-map.index.md
+  map: .opencode/skills/openspec-archive-change/.pi-map.md
+- .opencode/skills/openspec-explore
+  index: .opencode/skills/openspec-explore/.pi-map.index.md
+  map: .opencode/skills/openspec-explore/.pi-map.md
+- .opencode/skills/openspec-propose
+  index: .opencode/skills/openspec-propose/.pi-map.index.md
+  map: .opencode/skills/openspec-propose/.pi-map.md
+## files
+## links
+index: .opencode/skills/.pi-map.index.md
+map: .opencode/skills/.pi-map.md
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,18 @@
+# .opencode/skills
+dir: .opencode/skills
+
+index: .opencode/skills/.pi-map.index.md
+
+## role
+Contains reusable skill modules that provide specific capabilities or integrations for the OpenCode agent framework.
+## files
+## arch
+Modular plugin-based architecture where each skill is a self-contained unit implementing standardized interfaces for dynamic discovery and loading by the agent core.
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-apply-change (index)
+dir: .opencode/skills/openspec-apply-change
+
+## role
+Provides a spec-driven AI skill that implements tasks from OpenSpec changes by applying structured modifications to a codebase.
+## parent
+index: .opencode/skills/.pi-map.index.md
+map: .opencode/skills/.pi-map.md
+## children
+-
+## files
+- SKILL.md
+## links
+index: .opencode/skills/openspec-apply-change/.pi-map.index.md
+map: .opencode/skills/openspec-apply-change/.pi-map.md
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-apply-change
+dir: .opencode/skills/openspec-apply-change
+
+index: .opencode/skills/openspec-apply-change/.pi-map.index.md
+
+## role
+Provides a spec-driven AI skill that implements tasks from OpenSpec changes by applying structured modifications to a codebase.
+## 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
+Skill-based modular architecture using markdown-defined capabilities with a workflow-driven pattern that separates specification parsing from implementation execution.
+## tags
+skill, defines, assistant, implementing, tasks, openspec, change, spec
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-archive-change (index)
+dir: .opencode/skills/openspec-archive-change
+
+## role
+Provides a skill definition for archiving completed changes in an experimental workflow using the openspec CLI.
+## parent
+index: .opencode/skills/.pi-map.index.md
+map: .opencode/skills/.pi-map.md
+## children
+-
+## files
+- SKILL.md
+## links
+index: .opencode/skills/openspec-archive-change/.pi-map.index.md
+map: .opencode/skills/openspec-archive-change/.pi-map.md
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-archive-change
+dir: .opencode/skills/openspec-archive-change
+
+index: .opencode/skills/openspec-archive-change/.pi-map.index.md
+
+## role
+Provides a skill definition for archiving completed changes in an experimental workflow using the openspec CLI.
+## files
+- SKILL.md | Defines a skill for archiving completed changes in an experimental workflow using the openspec CLI. | dep: openspec CLI, AskUserQuestion tool, Task tool, file system (mkdir, mv, read), JSON parsing
+## arch
+Single-file skill definition using markdown-based skill documentation pattern with CLI tool integration.
+## tags
+skill, defines, archiving, completed, changes, experimental, workflow, openspec
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-explore (index)
+dir: .opencode/skills/openspec-explore
+
+## role
+Defines a conversational AI skill that acts 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
+-
@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-explore
+dir: .opencode/skills/openspec-explore
+
+index: .opencode/skills/openspec-explore/.pi-map.index.md
+
+## role
+Defines a conversational AI skill that acts 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
+Markdown-based skill definition using persona/role-prompting pattern with structured behavioral guidelines for non-implementation exploratory conversations.
+## tags
+skill, defines, conversational, persona, explore, mode, thinking, partner
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-propose (index)
+dir: .opencode/skills/openspec-propose
+
+## role
+Defines a structured workflow skill for proposing new changes using the openspec CLI, generating proposal, design, and task artifacts 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
+-
@@ -0,0 +1,19 @@
+# .opencode/skills/openspec-propose
+dir: .opencode/skills/openspec-propose
+
+index: .opencode/skills/openspec-propose/.pi-map.index.md
+
+## role
+Defines a structured workflow skill for proposing new changes using the openspec CLI, generating proposal, design, and task artifacts 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 structured workflow patterns for CLI-driven artifact generation and dependency-ordered execution.
+## tags
+skill, defines, structured, workflow, proposing, new, changes, openspec
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,79 @@
+# . (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
+## 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
+-
@@ -0,0 +1,42 @@
+# .
+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/Redis data layer, Traefik reverse proxy for TLS termination, environment-based configuration pattern, and Makefile-driven development workflow.
+## tags
+docker, redis, git, application, postgresql, compose, traefik, project
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,23 @@
+# .stoneforge (index)
+dir: .stoneforge
+
+## role
+Hidden system directory storing runtime state, configuration, and version-control metadata 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
+-
@@ -0,0 +1,21 @@
+# .stoneforge
+dir: .stoneforge
+
+index: .stoneforge/.pi-map.index.md
+
+## role
+Hidden system directory storing runtime state, configuration, and version-control metadata 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 flat-file storage with YAML-based configuration, dotfile-based state tracking, and standard Git ignore patterns.
+## tags
+config, stores, timestamp, identifier, data, tracking, dashboard, was
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,20 @@
+# .stoneforge/sync (index)
+dir: .stoneforge/sync
+
+## role
+Distributed task coordination and ephemeral worker agent management for a multi-agent execution system.
+## parent
+index: .stoneforge/.pi-map.index.md
+map: .stoneforge/.pi-map.md
+## children
+-
+## files
+- dependencies.jsonl
+- elements.jsonl
+## links
+index: .stoneforge/sync/.pi-map.index.md
+map: .stoneforge/sync/.pi-map.md
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,20 @@
+# .stoneforge/sync
+dir: .stoneforge/sync
+
+index: .stoneforge/sync/.pi-map.index.md
+
+## role
+Distributed task coordination and ephemeral worker agent management for a multi-agent execution 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 graph tracking, session-based worker lifecycle management, and decentralized worktree assignment.
+## tags
+stores, relationships, dependencies, elements, sequence, dependency, entities, json
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,23 @@
+# apps (index)
+dir: apps
+
+## role
+Contains the main application entry points and executable modules for 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
+-
@@ -0,0 +1,18 @@
+# apps
+dir: apps
+
+index: apps/.pi-map.index.md
+
+## role
+Contains the main application entry points and executable modules for the project.
+## files
+## arch
+Follows a modular application structure with separate directories for each deployable application, typically using framework-specific patterns (e.g., MVC, MVVM, or component-based architecture depending on the stack).
+## tags
+-
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,45 @@
+# apps/api (index)
+dir: apps/api
+
+## role
+Backend API service that provides a self-hosted FastAPI server for managing development projects, git repositories, and containerized tools via Docker.
+## parent
+index: apps/.pi-map.index.md
+map: apps/.pi-map.md
+## children
+- 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/.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
+-
@@ -0,0 +1,25 @@
+# apps/api
+dir: apps/api
+
+index: apps/api/.pi-map.index.md
+
+## role
+Backend API service that provides a self-hosted FastAPI server for managing development projects, git repositories, and containerized tools via Docker.
+## 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
+Modern Python async architecture using FastAPI with SQLAlchemy/alembic for PostgreSQL, uv for dependency management, multi-stage Docker builds with Cloudflare tunneling, and health-check orchestration for database readiness.
+## tags
+docker, alembic, python, database, fastapi, postgresql, asyncpg, uvicorn
+## symbols
+-
+## workflows
+-
+## dirty
+-
@@ -0,0 +1,25 @@
+# apps/api/alembic (index)
+dir: apps/api/alembic
+
+## role
+Database migration tooling that manages schema versioning and changes for the API's PostgreSQL database using Alembic with async SQLAlchemy.
+## parent
+index: apps/api/.pi-map.index.md
+map: apps/api/.pi-map.md
+## children
+- apps/api/alembic/versions
+  index: apps/api/alembic/versions/.pi-map.index.md
+  map: apps/api/alembic/versions/.pi-map.md
+## files
+- env.py
+- script.py.mako
+## links
+index: apps/api/alembic/.pi-map.index.md
+map: apps/api/alembic/.pi-map.md
+## workflows
+- change alembic behavior
+  read: env.py, script.py.mako
+- explore alembic subdirectories
+  index: apps/api/alembic/versions/.pi-map.index.md
+## dirty
+-
@@ -0,0 +1,23 @@
+# apps/api/alembic
+dir: apps/api/alembic
+
+index: apps/api/alembic/.pi-map.index.md
+
+## role
+Database migration tooling that manages schema versioning and changes for the API's PostgreSQL database using Alembic with async SQLAlchemy.
+## files
+- env.py | Configures Alembic database migration environment with async SQLAlchemy support for a project. | dep: alembic, sqlalchemy, sqlalchemy.ext.asyncio, logging.config, asyncio, src.config, src.models
+- script.py.mako | Alembic database migration script template that generates upgrade/downgrade functions for SQLAlchemy schema migrations | dep: alembic, sqlalchemy
+## arch
+Template-driven migration pattern using Alembic's declarative configuration with async engine setup, environment context management, and auto-generated revision scripts with upgrade/downgrade function pairs.
+## tags
+sqlalchemy, alembic, database, migration, asyncio, config, src, env
+## symbols
+-
+## workflows
+- change alembic behavior
+  read: env.py, script.py.mako
+- explore alembic subdirectories
+  index: apps/api/alembic/versions/.pi-map.index.md
+## dirty
+-
@@ -0,0 +1,67 @@
+# apps/api/alembic/versions (index)
+dir: apps/api/alembic/versions
+
+## role
+Database schema evolution management for the API application, tracking incremental changes to tables supporting users, authentication, projects, git repositories, tool types/instances, config profiles, workspaces, monitoring, and notifications.
+## parent
+index: apps/api/alembic/.pi-map.index.md
+map: apps/api/alembic/.pi-map.md
+## children
+-
+## 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
+- 398082499c30_add_tool_config_fields.py
+- 6fc7bfcf199f_merge_remove_is_builtin_and_add_config_.py
+- 86cec91fdb00_merge_profile_resolver_and_workspaces_.py
+- 8ed7dd80973d_create_config_folders_table.py
+- af8512103d67_add_tool_type_fields.py
+- f3d2dc90ba3a_merge_single_interface_and_clone_mode.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
+## dirty
+-
@@ -0,0 +1,74 @@
+# apps/api/alembic/versions
+dir: apps/api/alembic/versions
+
+index: apps/api/alembic/versions/.pi-map.index.md
+
+## role
+Database schema evolution management for the API application, tracking incremental changes to tables supporting users, authentication, projects, git repositories, tool types/instances, config profiles, workspaces, monitoring, and notifications.
+## 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 "pi-agent" terminal-based coding tool type to a tool_types table with Docker configuration templates | 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-related columns to tool_types and tool_instances, and migrates existing pi-agent data from Dockerfile templates to JSON-based manifest definitions | 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
+- 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
+- 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
+## arch
+Linear and branched Alembic migration pattern with merge migrations to reconcile divergent branches, using incremental revision files with upgrade/downgrade functions, idempotent operations, and occasional data migrations for schema transformations.
+## tags
+column, table, call:op.drop, key, alembic, downgrade, upgrade, constraint
+## 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
+## dirty
+-
@@ -0,0 +1,54 @@
+# apps/api/src (index)
+dir: apps/api/src
+
+## role
+Core application package that bootstraps and configures the Headquarter API FastAPI service with its infrastructure concerns.
+## 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
+-
@@ -0,0 +1,35 @@
+# apps/api/src
+dir: apps/api/src
+
+index: apps/api/src/.pi-map.index.md
+
+## role
+Core application package that bootstraps and configures the Headquarter API FastAPI service with its infrastructure concerns.
+## files
+- __init__.py | Marks the directory as a Python package for the Headquarter API.
+- config.py | Defines application configuration settings using Pydantic with environment variable loading, database URL construction, and computed properties for service URLs and OAuth endpoints. | exp: class:Settings, func:build_database_url(user: str, password: str, host: str, port: int, database: str) → str | dep: pydantic, pydantic_settings
+- database.py | Configures async SQLAlchemy database engine and session factory, and provides retry logic for database initialization with Alembic migrations via subprocess. | exp: func:init_database(max_retries, retry_delay) → bool, call:range, call:engine.connect, call:test_conn.execute, call:text, call:test_conn.close, call:logger.info, call:asyncio.get_event_loop().run_in_executor, call:subprocess.run, call:logger.debug, call:logger.error, call:asyncio.sleep, call:str(exc).lower, call:logger.warning | dep: asyncio, logging, 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 configuration with Pydantic settings, async SQLAlchemy with Alembic migration integration, structured JSON logging with correlation ID tracking, and FastAPI middleware/routing setup.
+## 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
+-
@@ -0,0 +1,40 @@
+# apps/api/src/api (index)
+dir: apps/api/src/api
+
+## role
+Defines reusable API validation utilities and package structure for FastAPI router organization.
+## 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
+-
@@ -0,0 +1,30 @@
+# apps/api/src/api
+dir: apps/api/src/api
+
+index: apps/api/src/api/.pi-map.index.md
+
+## role
+Defines reusable API validation utilities and package structure for FastAPI router organization.
+## 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 utility package with shared Pydantic validators for cross-cutting API schema concerns, following separation of validation logic from route handlers.
+## 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
+-
@@ -0,0 +1,24 @@
+# apps/api/src/api/config (index)
+dir: apps/api/src/api/config
+
+## role
+Exposes REST API endpoints for managing user configuration profiles and settings.
+## parent
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- config_profiles.py
+- user_config.py
+## links
+index: apps/api/src/api/config/.pi-map.index.md
+map: apps/api/src/api/config/.pi-map.md
+## workflows
+- change config behavior
+  read: __init__.py, config_profiles.py, user_config.py
+- change config config
+  read: config_profiles.py, user_config.py
+## dirty
+-
@@ -0,0 +1,31 @@
+# apps/api/src/api/config
+dir: apps/api/src/api/config
+
+index: apps/api/src/api/config/.pi-map.index.md
+
+## role
+Exposes REST API endpoints for managing user configuration profiles and settings.
+## 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
+FastAPI router modules following domain-driven separation with CRUD patterns, validation logic, and automatic default initialization.
+## 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
+-
@@ -1,10 +1,7 @@
 """Config profile API endpoints."""

 import logging
-import os
-import subprocess
 import uuid
-from typing import Any

 from fastapi import APIRouter, Depends, HTTPException, Query, status
 from sqlalchemy import select
@@ -12,10 +9,7 @@ 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
-from src.models.project import Project
-from src.models import ToolType
-from src.models import UserConfig
+from src.models import ConfigProfile, ConfigProfileInclude, UserConfig
 from src.schemas.config import (
    ConfigProfileCreate,
    ConfigProfileIncludeUpdate,
@@ -27,125 +21,27 @@ from src.schemas.config import (
 )
 from src.services.config.config_profile_resolver import (
    ConfigProfileCycleError,
-    check_include_cycle,
    resolve_profile,
    resolved_profile_to_dict,
 )
-from src.utils.git_url_parser import parse_git_url
+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"])

-MAX_PROFILE_SIZE_MB = 10
-MAX_PROFILE_SIZE_BYTES = MAX_PROFILE_SIZE_MB * 1024 * 1024
-
-
-def _calculate_profile_size(data: dict) -> int:
-    """Calculate approximate serialized size of profile data."""
-    total = 0
-    for key, value in data.get("env_vars", {}).items():
-        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
-    for key, value in data.get("runtime_hints", {}).items():
-        total += len(key.encode("utf-8")) + len(str(value).encode("utf-8"))
-    for mount in data.get("mounts", []):
-        total += len(str(mount.get("target", "")).encode("utf-8"))
-        total += len(str(mount.get("mode", "")).encode("utf-8"))
-        for path, content in mount.get("files", {}).items():
-            total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
-    for path, content in data.get("files", {}).items():
-        total += len(path.encode("utf-8")) + len(content.encode("utf-8"))
-    return total
-
-
-async def _get_profile_with_includes(
-    session: AsyncSession, profile_id: uuid.UUID
-) -> ConfigProfile | None:
-    """Fetch a profile with includes eagerly loaded."""
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile_id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    return result.scalar_one_or_none()
-
-
-async def _check_access(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    project_id: uuid.UUID | None = None,
-    tool_type_id: uuid.UUID | None = None,
-) -> None:
-    """Verify user has access to referenced project and tool type."""
-    if project_id is not None:
-        project = await session.get(Project, project_id)
-        if project is None:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND, detail="Project not found"
-            )
-        # Add ownership check if needed; for now just verify existence
-    if tool_type_id is not None:
-        tool_type = await session.get(ToolType, tool_type_id)
-        if tool_type is None:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND, detail="Tool type not found"
-            )
-
-
-async def _validate_git_mounts(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    git_mounts: list[Any],
-    project_id: uuid.UUID | None = None,
-) -> None:
-    """Validate git mount URLs.
-
-    Simply checks that remote_url looks like a valid git URL.
-    Actual clone validation happens at instance startup time.
-    """
-    for mount in git_mounts:
-        remote_url = mount.get("remote_url")
-        if not remote_url:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Git mount missing remote_url",
-            )
-
-        if not remote_url.startswith(("http://", "https://", "git@", "ssh://")):
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail=f"Invalid git URL: {remote_url}",
-            )
-
-
-def _profile_to_response(
-    profile: ConfigProfile, includes: list[ConfigProfileInclude] | None = None
-) -> dict:
-    return {
-        "id": str(profile.id),
-        "user_id": str(profile.user_id),
-        "name": profile.name,
-        "description": profile.description,
-        "project_id": str(profile.project_id) if profile.project_id else None,
-        "tool_type_id": str(profile.tool_type_id) if profile.tool_type_id else None,
-        "env_vars": profile.env_vars or {},
-        "runtime_hints": profile.runtime_hints or {},
-        "mounts": profile.mounts or [],
-        "git_mounts": profile.git_mounts or [],
-        "files": profile.files or {},
-        "is_default": profile.is_default,
-        "includes": [
-            {
-                "id": str(inc.id),
-                "included_profile_id": str(inc.included_profile_id),
-                "order_index": inc.order_index,
-            }
-            for inc in (includes or profile.includes)
-        ],
-        "created_at": profile.created_at.isoformat() if profile.created_at else None,
-        "updated_at": profile.updated_at.isoformat() if profile.updated_at else None,
-    }
-

@router.get("", response_model=list[ConfigProfileResponse])
 async def list_config_profiles(
@@ -165,26 +61,21 @@ async def list_config_profiles(
    )

    if project_id or tool_type_id:
-        # Compatibility filter: include portable profiles and matching scoped profiles
+        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

-        from sqlalchemy import or_
-
        conditions: list = []
-        # Portable profiles (no project, no tool)
        conditions.append(
            (ConfigProfile.project_id.is_(None))
            & (ConfigProfile.tool_type_id.is_(None))
        )
        if project_uuid:
-            # Profiles matching this project (with or without tool)
            conditions.append(ConfigProfile.project_id == project_uuid)
        if tool_uuid:
-            # Profiles matching this tool (with or without project)
            conditions.append(ConfigProfile.tool_type_id == tool_uuid)
        if project_uuid and tool_uuid:
-            # Exact match
            conditions.append(
                (ConfigProfile.project_id == project_uuid)
                & (ConfigProfile.tool_type_id == tool_uuid)
@@ -194,7 +85,7 @@ async def list_config_profiles(

    result = await session.execute(query)
    profiles = result.scalars().all()
-    return [_profile_to_response(p) for p in profiles]
+    return [profile_to_response(p) for p in profiles]


@router.post(
@@ -206,69 +97,9 @@ async def create_config_profile(
    session: AsyncSession = Depends(get_db_session),
 ):
    """Create a new config profile."""
-    user_uuid = current_user_id
-
-    # Check for duplicate name
-    existing = await session.execute(
-        select(ConfigProfile)
-        .where(
-            ConfigProfile.user_id == user_uuid,
-            ConfigProfile.name == data.name,
-        )
-        .options(selectinload(ConfigProfile.includes))
-    )
-    if existing.scalar_one_or_none() is not None:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"Profile with name '{data.name}' already exists",
-        )
-
-    # Validate references
-    project_uuid = uuid.UUID(data.project_id) if data.project_id else None
-    tool_uuid = uuid.UUID(data.tool_type_id) if data.tool_type_id else None
-    await _check_access(session, user_uuid, project_uuid, tool_uuid)
-
-    # Validate git mounts reference existing repositories
-    if data.git_mounts:
-        git_mounts_data = [
-            m.model_dump() if hasattr(m, "model_dump") else m for m in data.git_mounts
-        ]
-        await _validate_git_mounts(session, user_uuid, git_mounts_data, project_uuid)
-
-    # Check size
-    size = _calculate_profile_size(data.model_dump())
-    if size > MAX_PROFILE_SIZE_BYTES:
-        raise HTTPException(
-            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
-            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
-        )
-
-    profile = ConfigProfile(
-        user_id=user_uuid,
-        name=data.name,
-        description=data.description,
-        project_id=project_uuid,
-        tool_type_id=tool_uuid,
-        env_vars=data.env_vars,
-        runtime_hints=data.runtime_hints,
-        mounts=[m.model_dump() for m in data.mounts],
-        git_mounts=[m.model_dump() for m in data.git_mounts],
-        files=data.files,
-        is_default=data.is_default,
-    )
-    session.add(profile)
-    await session.commit()
-
-    # Re-fetch with includes to avoid lazy loading issues
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile.id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    profile = result.scalar_one()
-
-    logger.debug("Created config profile %s for user %s", profile.id, user_uuid)
-    return _profile_to_response(profile)
+    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)
@@ -278,7 +109,7 @@ async def get_config_profile(
    session: AsyncSession = Depends(get_db_session),
 ):
    """Get a config profile by ID."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_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"
@@ -287,7 +118,7 @@ async def get_config_profile(
        raise HTTPException(
            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
        )
-    return _profile_to_response(profile)
+    return profile_to_response(profile)


@router.put("/{profile_id}", response_model=ConfigProfileResponse)
@@ -298,7 +129,7 @@ async def update_config_profile(
    session: AsyncSession = Depends(get_db_session),
 ):
    """Update a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_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"
@@ -308,78 +139,9 @@ async def update_config_profile(
            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
        )

-    update_data = data.model_dump(exclude_unset=True)
-
-    # Handle name uniqueness
-    if "name" in update_data:
-        existing = await session.execute(
-            select(ConfigProfile).where(
-                ConfigProfile.user_id == profile.user_id,
-                ConfigProfile.name == update_data["name"],
-                ConfigProfile.id != profile.id,
-            )
-        )
-        if existing.scalar_one_or_none() is not None:
-            raise HTTPException(
-                status_code=status.HTTP_409_CONFLICT,
-                detail=f"Profile with name '{update_data['name']}' already exists",
-            )
-
-    # Validate references
-    project_uuid = (
-        uuid.UUID(update_data["project_id"])
-        if "project_id" in update_data and update_data["project_id"]
-        else (profile.project_id if "project_id" not in update_data else None)
-    )
-    tool_uuid = (
-        uuid.UUID(update_data["tool_type_id"])
-        if "tool_type_id" in update_data and update_data["tool_type_id"]
-        else (profile.tool_type_id if "tool_type_id" not in update_data else None)
-    )
-    await _check_access(session, profile.user_id, project_uuid, tool_uuid)
-
-    # Validate git mounts reference existing repositories
-    if "git_mounts" in update_data and update_data["git_mounts"] is not None:
-        git_mounts_data = [
-            m.model_dump() if hasattr(m, "model_dump") else m
-            for m in update_data["git_mounts"]
-        ]
-        await _validate_git_mounts(
-            session, profile.user_id, git_mounts_data, project_uuid
-        )
-
-    # Check size
-    current_data = _profile_to_response(profile)
-    merged = {**current_data, **update_data}
-    size = _calculate_profile_size(merged)
-    if size > MAX_PROFILE_SIZE_BYTES:
-        raise HTTPException(
-            status_code=status.HTTP_413_REQUEST_ENTITY_TOO_LARGE,
-            detail=f"Profile size exceeds {MAX_PROFILE_SIZE_MB}MB limit",
-        )
-
-    # Apply updates
-    for field_name, value in update_data.items():
-        if field_name in ("project_id", "tool_type_id"):
-            value = uuid.UUID(value) if value else None
-        elif field_name == "mounts" and value is not None:
-            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
-        elif field_name == "git_mounts" and value is not None:
-            value = [m.model_dump() if not isinstance(m, dict) else m for m in value]
-        setattr(profile, field_name, value)
-
-    await session.commit()
-
-    # Re-fetch with includes to avoid lazy loading issues
-    result = await session.execute(
-        select(ConfigProfile)
-        .where(ConfigProfile.id == profile.id)
-        .options(selectinload(ConfigProfile.includes))
-    )
-    profile = result.scalar_one()
-
+    profile = await update_profile(session, profile, data)
    logger.debug("Updated config profile %s", profile.id)
-    return _profile_to_response(profile)
+    return profile_to_response(profile)


@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
@@ -389,7 +151,7 @@ async def delete_config_profile(
    session: AsyncSession = Depends(get_db_session),
 ):
    """Delete a config profile."""
-    profile = await _get_profile_with_includes(session, uuid.UUID(profile_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"
@@ -407,14 +169,14 @@ async def delete_config_profile(


@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
-async def update_profile_includes(
+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))
+    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"
@@ -424,69 +186,8 @@ async def update_profile_includes(
            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
        )

-    # Validate all included profiles exist and belong to the user
    included_uuids = [uuid.UUID(inc_id) for inc_id in data.includes]
-    for inc_uuid in included_uuids:
-        inc_profile = await session.get(ConfigProfile, inc_uuid)
-        if inc_profile is None:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"Included profile not found: {inc_uuid}",
-            )
-        if inc_profile.user_id != current_user_id:
-            raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN,
-                detail=f"Not authorized to include profile: {inc_uuid}",
-            )
-        if inc_uuid == profile.id:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail="Profile cannot include itself",
-            )
-
-    # Check for cycles
-    cycle = await check_include_cycle(session, profile.id, None)
-    if cycle is None and included_uuids:
-        # Check each new include would not create a cycle
-        for inc_uuid in included_uuids:
-            cycle = await check_include_cycle(session, profile.id, inc_uuid)
-            if cycle is not None:
-                break
-
-    if cycle is not None:
-        cycle_str = " -> ".join(str(c) for c in cycle)
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"Include cycle detected: {cycle_str}",
-        )
-
-    # Remove existing includes
-    result = await session.execute(
-        select(ConfigProfileInclude).where(
-            ConfigProfileInclude.profile_id == profile.id
-        )
-    )
-    for existing in result.scalars().all():
-        await session.delete(existing)
-    await session.flush()
-
-    # Add new includes
-    for order_index, inc_uuid in enumerate(included_uuids):
-        include = ConfigProfileInclude(
-            profile_id=profile.id,
-            included_profile_id=inc_uuid,
-            order_index=order_index,
-        )
-        session.add(include)
-    await session.flush()
-
-    await session.commit()
-
-    # Re-fetch profile (includes loaded separately due to SQLite async issue)
-    result = await session.execute(
-        select(ConfigProfile).where(ConfigProfile.id == profile.id)
-    )
-    profile = result.scalar_one()
+    profile = await update_includes(session, profile, included_uuids, current_user_id)

    inc_result = await session.execute(
        select(ConfigProfileInclude).where(
@@ -496,7 +197,7 @@ async def update_profile_includes(
    direct_includes = inc_result.scalars().all()

    logger.debug("Updated includes for config profile %s", profile.id)
-    return _profile_to_response(profile, list(direct_includes))
+    return profile_to_response(profile, list(direct_includes))


@router.get("/{profile_id}/preview")
@@ -506,7 +207,7 @@ async def preview_config_profile(
    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))
+    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"
@@ -528,120 +229,19 @@ async def preview_config_profile(


@router.get("/defaults/resolve")
-async def resolve_default_profile(
+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.
-
-    Selects by specificity:
-    1. project+tool explicit default
-    2. project explicit default
-    3. tool explicit default
-    4. global/user explicit default
-    5. first created compatible profile
-    6. none (returns null)
-    """
-    user_uuid = current_user_id
-    project_uuid = uuid.UUID(project_id)
-    tool_uuid = uuid.UUID(tool_type_id)
-
-    # Fetch all compatible profiles ordered by created_at
-    query = (
-        select(ConfigProfile)
-        .where(ConfigProfile.user_id == user_uuid)
-        .where(
-            (ConfigProfile.project_id.is_(None) & ConfigProfile.tool_type_id.is_(None))
-            | (ConfigProfile.project_id == project_uuid)
-            | (ConfigProfile.tool_type_id == tool_uuid)
-            | (
-                (ConfigProfile.project_id == project_uuid)
-                & (ConfigProfile.tool_type_id == tool_uuid)
-            )
-        )
-        .order_by(ConfigProfile.created_at)
+    """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),
    )
-    result = await session.execute(query)
-    profiles = result.scalars().all()
-
-    if not profiles:
-        return {"profile_id": None, "profile_name": None}
-
-    # Check explicit defaults by specificity
-    explicit_defaults = [p for p in profiles if p.is_default]
-
-    # Most specific: project+tool
-    for p in explicit_defaults:
-        if p.project_id == project_uuid and p.tool_type_id == tool_uuid:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Next: project only
-    for p in explicit_defaults:
-        if p.project_id == project_uuid and p.tool_type_id is None:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Next: tool only
-    for p in explicit_defaults:
-        if p.project_id is None and p.tool_type_id == tool_uuid:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Next: global/user (no project, no tool)
-    for p in explicit_defaults:
-        if p.project_id is None and p.tool_type_id is None:
-            return {"profile_id": str(p.id), "profile_name": p.name}
-
-    # Fall back to first created compatible profile
-    first = profiles[0]
-    return {"profile_id": str(first.id), "profile_name": first.name}
-
-
-# ---------------------------------------------------------------------------
-# Default profile management
-# ---------------------------------------------------------------------------
-
-
-async def _get_or_create_user_config(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-) -> UserConfig:
-    """Get existing user config or create a new one."""
-    result = await session.execute(
-        select(UserConfig).where(UserConfig.user_id == user_id)
-    )
-    user_config = result.scalar_one_or_none()
-    if user_config is None:
-        user_config = UserConfig(user_id=user_id, config={})
-        session.add(user_config)
-    return user_config
-
-
-async def _validate_default_profiles(
-    session: AsyncSession,
-    user_id: uuid.UUID,
-    default_profiles: dict[str, str],
-) -> None:
-    """Validate that all profile IDs in default_profiles belong to the user."""
-    for tool_type_id, profile_id_str in default_profiles.items():
-        try:
-            profile_uuid = uuid.UUID(profile_id_str)
-        except ValueError:
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST,
-                detail=f"Invalid profile ID for tool type {tool_type_id}: {profile_id_str}",
-            )
-        profile = await session.get(ConfigProfile, profile_uuid)
-        if profile is None:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"Profile not found: {profile_id_str}",
-            )
-        if profile.user_id != user_id:
-            raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN,
-                detail=f"Profile does not belong to user: {profile_id_str}",
-            )


@router.get("/defaults")
@@ -664,8 +264,8 @@ async def set_default_profiles_endpoint(
    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)
+    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,
@@ -691,152 +291,10 @@ async def get_default_profile_for_tool_type_endpoint(


@router.post("/validate-git-url", response_model=ValidateGitUrlResponse)
-async def validate_git_url(
+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.
-
-    Parses the URL, suggests corrections for browser URLs, and runs
-    git ls-remote to verify reachability and enumerate branches.
-    """
-    parse_result = parse_git_url(data.url)
-    original_url = data.url.strip()
-    url_to_check = parse_result.get("base_url") or original_url
-
-    if not url_to_check:
-        return ValidateGitUrlResponse(
-            valid=False,
-            error=parse_result.get("message", "Invalid URL"),
-            error_code=parse_result.get("error_code", "INVALID_URL"),
-        )
-
-    # If the URL needed parsing, return suggestion without checking remote
-    if parse_result.get("needs_parsing") and url_to_check != original_url:
-        return ValidateGitUrlResponse(
-            valid=False,
-            suggested_url=url_to_check,
-            error=parse_result.get("message"),
-            error_code=parse_result.get("error_code", "URL_NEEDS_PARSING"),
-        )
-
-    # Optional SSH key for private repos
-    env = None
-    key_path = None
-    if data.ssh_key_id:
-        from src.models import SSHKey
-        from src.services.shared.ssh_keys import _get_fernet
-
-        try:
-            ssh_key_uuid = uuid.UUID(data.ssh_key_id)
-        except ValueError:
-            return ValidateGitUrlResponse(
-                valid=False,
-                error="Invalid SSH key ID format",
-                error_code="INVALID_SSH_KEY",
-            )
-
-        ssh_key = await session.get(SSHKey, ssh_key_uuid)
-        if ssh_key is None or ssh_key.user_id != current_user_id:
-            return ValidateGitUrlResponse(
-                valid=False,
-                error="SSH key not found or not authorized",
-                error_code="SSH_KEY_NOT_FOUND",
-            )
-
-        import tempfile
-
-        fernet = _get_fernet()
-        private_key = fernet.decrypt(ssh_key.private_key_encrypted.encode()).decode()
-        fd, key_path = tempfile.mkstemp(prefix="ssh_key_")
-        try:
-            os.write(fd, private_key.encode())
-        finally:
-            os.close(fd)
-        os.chmod(key_path, 0o600)
-        env = {
-            "GIT_SSH_COMMAND": f"ssh -i {key_path} -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
-        }
-
-    try:
-        result = subprocess.run(
-            ["git", "ls-remote", "--heads", url_to_check],
-            capture_output=True,
-            text=True,
-            timeout=30,
-            env={**os.environ, **env} if env else None,
-        )
-    except subprocess.TimeoutExpired:
-        if key_path and os.path.exists(key_path):
-            os.unlink(key_path)
-        return ValidateGitUrlResponse(
-            valid=False,
-            error="Remote repository check timed out",
-            error_code="TIMEOUT",
-        )
-    except FileNotFoundError:
-        if key_path and os.path.exists(key_path):
-            os.unlink(key_path)
-        return ValidateGitUrlResponse(
-            valid=False,
-            error="git command not found on server",
-            error_code="GIT_NOT_FOUND",
-        )
-    finally:
-        if key_path and os.path.exists(key_path):
-            os.unlink(key_path)
-
-    if result.returncode != 0:
-        stderr = result.stderr.strip()
-        if (
-            "could not resolve" in stderr.lower()
-            or "unable to access" in stderr.lower()
-        ):
-            error_msg = "Could not reach repository. Check the URL and network access."
-            error_code = "UNREACHABLE"
-        elif (
-            "authentication" in stderr.lower() or "permission denied" in stderr.lower()
-        ):
-            error_msg = (
-                "Authentication failed. Provide an SSH key for private repositories."
-            )
-            error_code = "AUTH_FAILED"
-        else:
-            error_msg = f"Repository not accessible: {stderr[:200]}"
-            error_code = "REMOTE_ERROR"
-        return ValidateGitUrlResponse(
-            valid=False,
-            error=error_msg,
-            error_code=error_code,
-        )
-
-    # Parse branches from ls-remote output
-    branches: list[str] = []
-    default_branch = "main"
-    for line in result.stdout.strip().split("\n"):
-        if not line.strip():
-            continue
-        parts = line.split()
-        if len(parts) == 2:
-            ref = parts[1]
-            # refs/heads/branch-name
-            if ref.startswith("refs/heads/"):
-                branch_name = ref[len("refs/heads/") :]
-                branches.append(branch_name)
-                if branch_name in ("main", "master"):
-                    default_branch = branch_name
-
-    if not branches:
-        return ValidateGitUrlResponse(
-            valid=False,
-            error="No branches found in remote repository",
-            error_code="NO_BRANCHES",
-        )
-
-    return ValidateGitUrlResponse(
-        valid=True,
-        suggested_url=url_to_check if url_to_check != original_url else None,
-        branches=branches,
-        default_branch=default_branch,
-    )
+    """Validate a git remote URL and list available branches."""
+    return await validate_git_url(session, current_user_id, data.url, data.ssh_key_id)
@@ -0,0 +1,22 @@
+# apps/api/src/api/project (index)
+dir: apps/api/src/api/project
+
+## role
+Provides REST API endpoints for project and Git repository management in the backend service.
+## parent
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- git_repositories.py
+- projects.py
+## links
+index: apps/api/src/api/project/.pi-map.index.md
+map: apps/api/src/api/project/.pi-map.md
+## workflows
+- change project behavior
+  read: __init__.py, git_repositories.py, projects.py
+## dirty
+-
@@ -0,0 +1,26 @@
+# 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, events, 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
+-
@@ -0,0 +1,33 @@
+# 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, events, 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 modular router pattern with separate files per domain concern, combining REST endpoints, SSE streaming, WebSocket connections, and HTTP proxying; uses dependency injection for auth and integrates with Docker/container runtime for terminal and instance proxy features.
+## 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
+-
@@ -0,0 +1,26 @@
+# apps/api/src/api/tool (index)
+dir: apps/api/src/api/tool
+
+## role
+Provides FastAPI REST API endpoints and routers for managing the complete lifecycle of Docker-based tools, including type definitions, instances, sessions, and lifecycle operations.
+## parent
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- sessions.py
+- tool_definitions.py
+- tool_instances.py
+- tool_lifecycle.py
+- tool_types.py
+- tool_types_validation.py
+## links
+index: apps/api/src/api/tool/.pi-map.index.md
+map: apps/api/src/api/tool/.pi-map.md
+## workflows
+- change tool behavior
+  read: __init__.py, sessions.py, tool_definitions.py
+## dirty
+-
@@ -0,0 +1,33 @@
+# apps/api/src/api/tool
+dir: apps/api/src/api/tool
+
+index: apps/api/src/api/tool/.pi-map.index.md
+
+## role
+Provides FastAPI REST API endpoints and routers for managing the complete lifecycle of Docker-based tools, including type definitions, instances, sessions, and lifecycle operations.
+## 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 | API endpoint that retrieves 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
+- 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, checking required structure, verifying port exposure, and ensuring required variables are present. | 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, func:validate_required_variables(template: str, variables: list[str]) → None, raise:HTTPException | dep: re, yaml, fastapi, fastapi.HTTPException, fastapi.status
+## arch
+Modular FastAPI router composition pattern with separated concerns across CRUD operations, validation, lifecycle management, and proxying, aggregated through `__init__.py` for unified module interface.
+## 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
+-
@@ -3,11 +3,13 @@
 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",
 ]
@@ -53,6 +53,13 @@ async def get_user_sessions(
        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),
@@ -64,10 +71,9 @@ async def get_user_sessions(
                "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,
-                "clone_mode": instance.clone_mode,
-                "branch": instance.branch,
                "selected_config_profile_id": str(instance.selected_config_profile_id)
                if instance.selected_config_profile_id
                else None,
@@ -0,0 +1,135 @@
+"""Tool instance lifecycle API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import (
+    _get_owned_project,
+    _get_user,
+    get_current_user_id,
+    get_db_session,
+)
+from src.schemas.tool import StartInstanceRequest
+from src.services.tool.instance_service import (
+    delete_tool_instance,
+    restart_tool_instance,
+    start_tool_instance,
+    stop_tool_instance,
+)
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/projects", tags=["tool-instances"])
+
+
+@router.post(
+    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/start",
+    summary="Start instance",
+    description="Start a tool instance using Docker Compose.",
+)
+async def start_instance(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    instance_id: uuid.UUID,
+    data: StartInstanceRequest | None = None,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    _user = await _get_user(session, user_id)
+    _project = await _get_owned_project(project_id, user_id, session)
+    try:
+        return await start_tool_instance(
+            session, user_id, project_id, repo_id, instance_id, data
+        )
+    except ValueError as exc:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
+    except RuntimeError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
+        )
+
+
+@router.post(
+    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/stop",
+    summary="Stop instance",
+    description="Stop a running tool instance.",
+)
+async def stop_instance(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    instance_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    _user = await _get_user(session, user_id)
+    _project = await _get_owned_project(project_id, user_id, session)
+    try:
+        return await stop_tool_instance(session, user_id, project_id, repo_id, instance_id)
+    except ValueError as exc:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=str(exc))
+
+
+@router.post(
+    "/{project_id}/repositories/{repo_id}/instances/{instance_id}/restart",
+    summary="Restart instance",
+    description="Restart a tool instance.",
+)
+async def restart_instance(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    instance_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    _user = await _get_user(session, user_id)
+    _project = await _get_owned_project(project_id, user_id, session)
+    try:
+        return await restart_tool_instance(
+            session, user_id, project_id, repo_id, instance_id
+        )
+    except ValueError as exc:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc))
+    except RuntimeError as exc:
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=str(exc)
+        )
+
+
+@router.delete(
+    "/{project_id}/repositories/{repo_id}/instances/{instance_id}",
+    summary="Delete instance",
+    description="Delete a tool instance and remove its Docker containers and files.",
+)
+async def delete_instance(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    instance_id: uuid.UUID,
+    force: bool = False,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    _user = await _get_user(session, user_id)
+    _project = await _get_owned_project(project_id, user_id, session)
+    try:
+        await delete_tool_instance(
+            session, user_id, project_id, repo_id, instance_id, force
+        )
+    except ValueError as exc:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=str(exc))
+    except RuntimeError as exc:
+        detail = str(exc)
+        if "uncommitted changes" in detail.lower():
+            raise HTTPException(
+                status_code=status.HTTP_409_CONFLICT,
+                detail={
+                    "message": "Repository has uncommitted changes",
+                    "changed_files": detail,
+                    "force_required": True,
+                },
+            )
+        raise HTTPException(
+            status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=detail
+        )
@@ -0,0 +1,23 @@
+# apps/api/src/api/user (index)
+dir: apps/api/src/api/user
+
+## role
+Provides user-facing API endpoints for authentication, profile management, and SSH key operations in a FastAPI backend application.
+## parent
+index: apps/api/src/api/.pi-map.index.md
+map: apps/api/src/api/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- auth.py
+- ssh_keys.py
+- users.py
+## links
+index: apps/api/src/api/user/.pi-map.index.md
+map: apps/api/src/api/user/.pi-map.md
+## workflows
+- change user behavior
+  read: __init__.py, auth.py, ssh_keys.py
+## dirty
+-
@@ -0,0 +1,30 @@
+# apps/api/src/api/user
+dir: apps/api/src/api/user
+
+index: apps/api/src/api/user/.pi-map.index.md
+
+## role
+Provides user-facing API endpoints for authentication, profile management, and SSH key operations in a FastAPI backend application.
+## 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 separate submodule files per domain concern (auth, SSH keys, users), aggregated via __init__.py, using OAuth2/OIDC external identity provider (Authentik) and encrypted key storage for cryptographic operations.
+## tags
+user, get, call:, key, ssh, src, cookie, raise:httpexception
+## symbols
+- get_db_session
+- login
+- callback
+- logout
+- me
+- _get_fernet
+- generate_ssh_key_pair
+- create_ssh_key
+## workflows
+- change user behavior
+  read: __init__.py, auth.py, ssh_keys.py
+## dirty
+-
@@ -0,0 +1,24 @@
+# apps/api/src/api/workspace (index)
+dir: apps/api/src/api/workspace
+
+## role
+Provides FastAPI REST endpoints for workspace management, file operations, and git integration in 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
+-
@@ -0,0 +1,31 @@
+# apps/api/src/api/workspace
+dir: apps/api/src/api/workspace
+
+index: apps/api/src/api/workspace/.pi-map.index.md
+
+## role
+Provides FastAPI REST endpoints for workspace management, file operations, and git integration in 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 | Defines API endpoints for listing tool instances associated with a specific workspace, verifying workspace ownership. | 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_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
+- workspaces.py | Provides FastAPI CRUD endpoints for managing Git repository workspaces with nested and top-level URL structures, including listing, creating, updating, deleting, and syncing workspaces with instance count tracking. | 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.name.label("repo_name"), GitRepository.project_id, GitRepository.ssh_key_id.label("repo_ssh_key_id"), instance_count.label("instance_count"), ) .join(GitRepository, Workspace.repo_id == GitRepository.id) .where(Workspace.user_id == user_id) .order_by, call:GitRepository.name.label, call:GitRepository.ssh_key_id.label, 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: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 composition with domain-separated endpoint modules (files, git, instances, workspaces) using FastAPI dependency injection for workspace ownership verification and nested resource URL patterns.
+## 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
+-
@@ -2,13 +2,16 @@

 import uuid

-from fastapi import APIRouter, Depends, HTTPException
+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")

@@ -30,6 +33,63 @@ async def _get_workspace(
    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,
@@ -0,0 +1,24 @@
+# apps/api/src/auth (index)
+dir: apps/api/src/auth
+
+## role
+Provides authentication and authorization infrastructure for the API, including OIDC/OAuth2 integration, session management, and FastAPI dependency injection.
+## parent
+index: apps/api/src/.pi-map.index.md
+map: apps/api/src/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- cookies.py
+- dependencies.py
+- oidc.py
+- session.py
+## links
+index: apps/api/src/auth/.pi-map.index.md
+map: apps/api/src/auth/.pi-map.md
+## workflows
+- change auth behavior
+  read: __init__.py, cookies.py, dependencies.py
+## dirty
+-
@@ -0,0 +1,31 @@
+# apps/api/src/auth
+dir: apps/api/src/auth
+
+index: apps/api/src/auth/.pi-map.index.md
+
+## role
+Provides authentication and authorization infrastructure for the API, including OIDC/OAuth2 integration, session management, and FastAPI dependency injection.
+## files
+- __init__.py | Re-exports authentication utility functions from submodules to provide a unified public API for the auth package | dep: src.auth.cookies, src.auth.oidc, src.auth.session
+- cookies.py | Builds a dictionary of HTTP cookie options from application settings for secure cookie configuration. | exp: func:build_cookie_options(settings: Settings) → dict[str, str | bool | None] | dep: src.config, src.config.Settings
+- dependencies.py | Provides FastAPI dependency functions for database sessions, user authentication, and project authorization. | exp: func:get_db_session(), call:SessionLocal, func:get_current_user_id(session_cookie) → uuid.UUID, call:Settings, call:decode_session_cookie, call:uuid.UUID, call:str, raise:HTTPException, func:get_current_user(session_cookie, db_session) → User, call:Settings, call:decode_session_cookie, call:uuid.UUID, call:str, call:db_session.get, raise:HTTPException, func:_get_user(session: AsyncSession, user_id: uuid.UUID) → User, call:session.get, raise:HTTPException, func:_get_owned_project(project_id: uuid.UUID, user_id: uuid.UUID, session: AsyncSession) → "Project", call:session.get, raise:HTTPException | dep: uuid, typing, fastapi, sqlalchemy.ext.asyncio, src.auth.session, src.config, src.database, src.models.project, src.models.user, sqlalchemy
+- oidc.py | Implements OIDC/OAuth2 authentication flow with Authentik, including login URL construction, authorization code exchange for tokens, and user info retrieval. | exp: func:build_login_redirect_url(settings: Settings, redirect_uri: str, state: str) → str, call:urlencode, func:exchange_code_for_tokens(settings: Settings, code: str, redirect_uri: str, client: httpx.AsyncClient) → dict[str, str], call:client.post, call:response.raise_for_status, call:response.json, call:payload.get, func:fetch_user_info(settings: Settings, access_token: str, client: httpx.AsyncClient) → dict[str, Any], call:client.get, call:response.raise_for_status, call:response.json | dep: typing, urllib.parse, httpx, src.config
+- session.py | Implements creation and verification of signed session cookies using HMAC-SHA256 in a JWS-like format. | exp: func:_base64url_encode(data: bytes) → str, call:base64.urlsafe_b64encode(data).rstrip(b"=").decode, func:_base64url_decode(data: str) → bytes, call:len, call:base64.urlsafe_b64decode, func:create_session_cookie(settings: Settings, user_id: str) → str, call:int, call:(datetime.now(timezone.utc) + timedelta(hours=settings.session_ttl_hours)).timestamp, call:datetime.now, call:timedelta, call:_base64url_encode, call:json.dumps({"alg": "HS256", "typ": "session"}).encode, call:json.dumps(payload).encode, call:hmac.new( settings.session_secret.encode(), message.encode(), hashlib.sha256, ).digest, call:settings.session_secret.encode, call:message.encode, func:decode_session_cookie(settings: Settings, cookie_value: str) → dict[str, Any], call:cookie_value.split, call:len, call:hmac.new( settings.session_secret.encode(), message.encode(), hashlib.sha256, ).digest, call:settings.session_secret.encode, call:message.encode, call:_base64url_encode, call:hmac.compare_digest, call:_base64url_decode, call:json.loads, call:payload.get, call:int, call:datetime.now(timezone.utc).timestamp, raise:ValueError | dep: hmac, hashlib, json, base64, datetime, typing, src.config, src.config.Settings
+## arch
+Modular utility package with separation of concerns across cookies, sessions, OIDC flows, and FastAPI dependencies; uses HMAC-SHA256 JWS-like tokens and external Authentik identity provider.
+## tags
+session, src, cookie, user, get, base64url, raise:httpexception, call:
+## symbols
+- build_cookie_options
+- get_db_session
+- get_current_user_id
+- get_current_user
+- _get_user
+- _get_owned_project
+- build_login_redirect_url
+- exchange_code_for_tokens
+## workflows
+- change auth behavior
+  read: __init__.py, cookies.py, dependencies.py
+## dirty
+-
@@ -21,6 +21,7 @@ from src.api.tool import (
    sessions_router,
    tool_definitions_router,
    tool_instances_router,
+    tool_lifecycle_router,
    tool_types_router,
 )
 from src.api.user import auth_router, ssh_keys_router, users_router
@@ -165,6 +166,7 @@ app.include_router(tool_types_router)
 app.include_router(tool_definitions_router)
 app.include_router(config_profiles_router)
 app.include_router(tool_instances_router)
+app.include_router(tool_lifecycle_router)
 app.include_router(sessions_router)
 app.include_router(instance_proxy_router)
 app.include_router(terminal_router)
@@ -0,0 +1,37 @@
+# apps/api/src/models (index)
+dir: apps/api/src/models
+
+## role
+Provides the core database model layer with a centralized public API, defining SQLAlchemy base classes and reusable mixins for consistent schema patterns across the API application.
+## parent
+index: apps/api/src/.pi-map.index.md
+map: apps/api/src/.pi-map.md
+## children
+- apps/api/src/models/config
+  index: apps/api/src/models/config/.pi-map.index.md
+  map: apps/api/src/models/config/.pi-map.md
+- apps/api/src/models/project
+  index: apps/api/src/models/project/.pi-map.index.md
+  map: apps/api/src/models/project/.pi-map.md
+- apps/api/src/models/system
+  index: apps/api/src/models/system/.pi-map.index.md
+  map: apps/api/src/models/system/.pi-map.md
+- apps/api/src/models/tool
+  index: apps/api/src/models/tool/.pi-map.index.md
+  map: apps/api/src/models/tool/.pi-map.md
+- apps/api/src/models/user
+  index: apps/api/src/models/user/.pi-map.index.md
+  map: apps/api/src/models/user/.pi-map.md
+## files
+- __init__.py
+- base.py
+## links
+index: apps/api/src/models/.pi-map.index.md
+map: apps/api/src/models/.pi-map.md
+## workflows
+- change models behavior
+  read: __init__.py, base.py
+- explore models subdirectories
+  index: apps/api/src/models/config/.pi-map.index.md, apps/api/src/models/project/.pi-map.index.md, apps/api/src/models/system/.pi-map.index.md
+## dirty
+-
@@ -0,0 +1,25 @@
+# apps/api/src/models
+dir: apps/api/src/models
+
+index: apps/api/src/models/.pi-map.index.md
+
+## role
+Provides the core database model layer with a centralized public API, defining SQLAlchemy base classes and reusable mixins for consistent schema patterns across the API application.
+## files
+- __init__.py | Re-exports model classes from submodules to provide a centralized public API for the src.models package | dep: src.models.base, src.models.config.config_profile, src.models.project.git_repository, src.models.project.project, src.models.project.workspace, src.models.system.health_check, src.models.system.instance_event, src.models.system.notification, src.models.system.terminal_session, src.models.tool.tool_definition_manifest, src.models.tool.tool_instance, src.models.tool.tool_type, src.models.user.ssh_key, src.models.user.user, src.models.user.user_config
+- base.py | Defines SQLAlchemy base model and reusable mixins for UUID primary keys and automatic timestamp tracking in database models. | exp: class:Base, class:UUIDPrimaryKeyMixin, class:TimestampMixin | dep: uuid, datetime, sqlalchemy, sqlalchemy.orm
+## arch
+Uses the declarative base pattern with mixin composition for cross-cutting concerns (UUIDs, timestamps), and a facade/aggregate module pattern via __init__.py re-exports to simplify imports for consumers.
+## tags
+models, src, base, project, system, user, mixin, tool
+## symbols
+- Base
+- UUIDPrimaryKeyMixin
+- TimestampMixin
+## workflows
+- change models behavior
+  read: __init__.py, base.py
+- explore models subdirectories
+  index: apps/api/src/models/config/.pi-map.index.md, apps/api/src/models/project/.pi-map.index.md, apps/api/src/models/system/.pi-map.index.md
+## dirty
+-
@@ -0,0 +1,23 @@
+# apps/api/src/models/config (index)
+dir: apps/api/src/models/config
+
+## role
+Provides SQLAlchemy ORM models for managing configuration profiles and their hierarchical includes in the API application.
+## parent
+index: apps/api/src/models/.pi-map.index.md
+map: apps/api/src/models/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- config_profile.py
+## links
+index: apps/api/src/models/config/.pi-map.index.md
+map: apps/api/src/models/config/.pi-map.md
+## workflows
+- change config behavior
+  read: __init__.py, config_profile.py
+- change config config
+  read: config_profile.py
+## dirty
+-
@@ -0,0 +1,24 @@
+# apps/api/src/models/config
+dir: apps/api/src/models/config
+
+index: apps/api/src/models/config/.pi-map.index.md
+
+## role
+Provides SQLAlchemy ORM models for managing configuration profiles and their hierarchical includes in the API application.
+## files
+- __init__.py | Exports config model classes from a subpackage for simplified importing | dep: src.models.config.config_profile
+- config_profile.py | Defines SQLAlchemy ORM models for configuration profiles and their includes, storing environment variables, runtime hints, mounts, files, and git mounts with user/project/tool associations and self-referential inclusion relationships. | exp: class:ConfigProfile, class:ConfigProfileInclude | dep: uuid, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models.project, src.models, src.models.user, src.models (ToolType)
+## arch
+Uses SQLAlchemy declarative ORM pattern with self-referential many-to-many relationships for profile inclusion, and associations to users, projects, and tools.
+## tags
+config, src, models, profile, sqlalchemy, init, orm, mounts
+## symbols
+- ConfigProfile
+- ConfigProfileInclude
+## workflows
+- change config behavior
+  read: __init__.py, config_profile.py
+- change config config
+  read: config_profile.py
+## dirty
+-
@@ -0,0 +1,23 @@
+# apps/api/src/models/project (index)
+dir: apps/api/src/models/project
+
+## role
+Defines the core data models for project-related entities (GitRepository, Project, Workspace) using SQLAlchemy ORM.
+## parent
+index: apps/api/src/models/.pi-map.index.md
+map: apps/api/src/models/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- git_repository.py
+- project.py
+- workspace.py
+## links
+index: apps/api/src/models/project/.pi-map.index.md
+map: apps/api/src/models/project/.pi-map.md
+## workflows
+- change project behavior
+  read: __init__.py, git_repository.py, project.py
+## dirty
+-
@@ -0,0 +1,25 @@
+# apps/api/src/models/project
+dir: apps/api/src/models/project
+
+index: apps/api/src/models/project/.pi-map.index.md
+
+## role
+Defines the core data models for project-related entities (GitRepository, Project, Workspace) using SQLAlchemy ORM.
+## files
+- __init__.py | Exports the three main project model classes (GitRepository, Project, Workspace) as the public API for the models.project package. | dep: src.models.project.git_repository, src.models.project.project, src.models.project.workspace
+- git_repository.py | Defines a SQLAlchemy ORM model for Git repositories with relationships to projects, users, and SSH keys. | exp: class:GitRepository | dep: uuid, datetime, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models.project, src.models, src.models.user, src.models.ssh_key
+- project.py | Defines a SQLAlchemy ORM model for a Project entity with relationships to users, Git repositories, and SSH keys. | exp: class:Project | dep: uuid, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models, src.models.user, src.models.GitRepository, src.models.SSHKey, src.models.user.User
+- workspace.py | Defines a SQLAlchemy ORM model for persistent writable Git repository clones associated with users. | exp: class:Workspace | dep: uuid, datetime, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models, src.models.user, src.models.GitRepository, src.models.user.User
+## arch
+Standard SQLAlchemy ORM pattern with declarative models, package-level public API abstraction via __init__.py, and bidirectional relationships between entities.
+## tags
+models, src, project, sqlalchemy, git, user, workspace, orm
+## symbols
+- GitRepository
+- Project
+- Workspace
+## workflows
+- change project behavior
+  read: __init__.py, git_repository.py, project.py
+## dirty
+-
@@ -0,0 +1,24 @@
+# apps/api/src/models/system (index)
+dir: apps/api/src/models/system
+
+## role
+Provides SQLAlchemy ORM models for system-level operational and audit data including health checks, instance events, notifications, and terminal sessions.
+## parent
+index: apps/api/src/models/.pi-map.index.md
+map: apps/api/src/models/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- health_check.py
+- instance_event.py
+- notification.py
+- terminal_session.py
+## links
+index: apps/api/src/models/system/.pi-map.index.md
+map: apps/api/src/models/system/.pi-map.md
+## workflows
+- change system behavior
+  read: __init__.py, health_check.py, instance_event.py
+## dirty
+-
@@ -0,0 +1,27 @@
+# apps/api/src/models/system
+dir: apps/api/src/models/system
+
+index: apps/api/src/models/system/.pi-map.index.md
+
+## role
+Provides SQLAlchemy ORM models for system-level operational and audit data including health checks, instance events, notifications, and terminal sessions.
+## files
+- __init__.py | Exports system-related model classes from a package for convenient importing. | dep: src.models.system.health_check, src.models.system.instance_event, src.models.system.notification, src.models.system.terminal_session
+- health_check.py | Defines a SQLAlchemy ORM model for storing health check snapshots of tool instances with various status and probe fields. | exp: class:HealthCheck | dep: uuid, datetime, sqlalchemy, sqlalchemy.orm, src.models.base
+- instance_event.py | Defines a SQLAlchemy ORM model for auditing instance lifecycle events with metadata, status tracking, and user attribution. | exp: class:InstanceEvent | dep: uuid, datetime, typing, sqlalchemy, sqlalchemy.orm, src.models.base
+- notification.py | Defines a SQLAlchemy ORM model for storing user notifications with metadata, read/dismissed tracking, and polymorphic source references. | exp: class:Notification | dep: datetime, typing, uuid, sqlalchemy, sqlalchemy.orm, sqlalchemy.sql, src.models.base
+- terminal_session.py | Defines a SQLAlchemy database model for storing terminal session metadata with lifecycle tracking. | exp: class:TerminalSessionModel | dep: uuid, datetime, sqlalchemy, sqlalchemy.orm, src.models.base
+## arch
+Standard SQLAlchemy declarative ORM pattern with timestamped base models, polymorphic relationships (notification sources), lifecycle state tracking, and audit fields (user attribution, status enums).
+## tags
+sqlalchemy, src, models, model, orm, system, notification, health
+## symbols
+- HealthCheck
+- InstanceEvent
+- Notification
+- TerminalSessionModel
+## workflows
+- change system behavior
+  read: __init__.py, health_check.py, instance_event.py
+## dirty
+-
@@ -0,0 +1,23 @@
+# apps/api/src/models/tool (index)
+dir: apps/api/src/models/tool
+
+## role
+Defines SQLAlchemy ORM models for managing tool definitions, instances, and types in a container-based deployment system.
+## parent
+index: apps/api/src/models/.pi-map.index.md
+map: apps/api/src/models/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- tool_definition_manifest.py
+- tool_instance.py
+- tool_type.py
+## links
+index: apps/api/src/models/tool/.pi-map.index.md
+map: apps/api/src/models/tool/.pi-map.md
+## workflows
+- change tool behavior
+  read: __init__.py, tool_definition_manifest.py, tool_instance.py
+## dirty
+-
@@ -0,0 +1,25 @@
+# apps/api/src/models/tool
+dir: apps/api/src/models/tool
+
+index: apps/api/src/models/tool/.pi-map.index.md
+
+## role
+Defines SQLAlchemy ORM models for managing tool definitions, instances, and types in a container-based deployment system.
+## files
+- __init__.py | Exports the public API for the tool models module by re-exporting three key classes. | dep: src.models.tool.tool_definition_manifest, src.models.tool.tool_instance, src.models.tool.tool_type
+- tool_definition_manifest.py | Defines a SQLAlchemy ORM model for storing tool definition manifests that compile to Dockerfiles and Compose files, supporting both base definitions and tool-specific definitions with inheritance. | exp: class:ToolDefinitionManifest | dep: uuid, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models.user
+- tool_instance.py | Defines a SQLAlchemy ORM model for tool instances that represent deployed tools with container/runtime metadata and relationships to users, projects, repositories, and workspaces. | exp: class:ToolInstance | dep: uuid, datetime, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models, src.models.project, src.models.user, src.models (ConfigProfile, GitRepository, Project, ToolType, User, Workspace)
+- tool_type.py | Defines a SQLAlchemy ORM model for tool types that represent configurable categories of tools with deployment templates, manifest references, and metadata. | exp: class:ToolType | dep: uuid, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models.tool.tool_definition_manifest, src.models.user
+## arch
+Domain-driven SQLAlchemy ORM models with inheritance patterns (base/tool-specific manifests), rich relationships (users, projects, repositories, workspaces), and template-based deployment abstractions.
+## tags
+tool, models, src, sqlalchemy, orm, definition, manifest, base
+## symbols
+- ToolDefinitionManifest
+- ToolInstance
+- ToolType
+## workflows
+- change tool behavior
+  read: __init__.py, tool_definition_manifest.py, tool_instance.py
+## dirty
+-
@@ -53,9 +53,11 @@ class ToolInstance(UUIDPrimaryKeyMixin, TimestampMixin, Base):
    )
    image_tag: Mapped[str | None] = mapped_column(String(256), nullable=True)
    probe_result: Mapped[dict | None] = mapped_column(JSON, nullable=True)
-    clone_mode: Mapped[str] = mapped_column(String(20), nullable=False, default="mount")
+    clone_mode: Mapped[str | None] = mapped_column(
+        String(20), nullable=True, default=None
+    )
    branch: Mapped[str | None] = mapped_column(
-        String(255), nullable=True, default="main"
+        String(255), nullable=True, default=None
    )
    selected_config_profile_id: Mapped[uuid.UUID | None] = mapped_column(
        UUID(), ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True
@@ -0,0 +1,25 @@
+# apps/api/src/models/user (index)
+dir: apps/api/src/models/user
+
+## role
+Provides the core data models for user identity, authentication credentials, and personal configuration in the API's database layer.
+## parent
+index: apps/api/src/models/.pi-map.index.md
+map: apps/api/src/models/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- ssh_key.py
+- user.py
+- user_config.py
+## links
+index: apps/api/src/models/user/.pi-map.index.md
+map: apps/api/src/models/user/.pi-map.md
+## workflows
+- change user behavior
+  read: __init__.py, ssh_key.py, user.py
+- change user config
+  read: user_config.py
+## dirty
+-
@@ -0,0 +1,27 @@
+# apps/api/src/models/user
+dir: apps/api/src/models/user
+
+index: apps/api/src/models/user/.pi-map.index.md
+
+## role
+Provides the core data models for user identity, authentication credentials, and personal configuration in the API's database layer.
+## files
+- __init__.py | Exports the user-related model classes (SSHKey, User, UserConfig) from a package for convenient importing. | dep: src.models.user.ssh_key, src.models.user.user, src.models.user.user_config
+- ssh_key.py | Defines an SSHKey SQLAlchemy ORM model for storing encrypted SSH key pairs with user and optional project associations. | exp: class:SSHKey | dep: uuid, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models.project, src.models.user
+- user.py | Defines a SQLAlchemy ORM model for a User entity with authentication fields and relationships to projects, SSH keys, and user configuration. | exp: class:User | dep: typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models.project, src.models, src.models.SSHKey, src.models.UserConfig
+- user_config.py | Defines a SQLAlchemy model for storing per-user JSON configuration with typed property accessors for default profile IDs. | exp: class:UserConfig | dep: uuid, typing, sqlalchemy, sqlalchemy.orm, src.models.base, src.models.user
+## arch
+Follows SQLAlchemy ORM declarative model pattern with package-level aggregation via __init__.py, using explicit table relationships (foreign keys, one-to-many associations) and a JSON-backed configuration store with typed property accessors.
+## tags
+user, src, models, sqlalchemy, sshkey, orm, model, ssh
+## symbols
+- SSHKey
+- User
+- UserConfig
+## workflows
+- change user behavior
+  read: __init__.py, ssh_key.py, user.py
+- change user config
+  read: user_config.py
+## dirty
+-
@@ -0,0 +1,36 @@
+# apps/api/src/schemas (index)
+dir: apps/api/src/schemas
+
+## role
+Defines Pydantic schemas for data validation, serialization, and API request/response models in the FastAPI application.
+## parent
+index: apps/api/src/.pi-map.index.md
+map: apps/api/src/.pi-map.md
+## children
+- apps/api/src/schemas/config
+  index: apps/api/src/schemas/config/.pi-map.index.md
+  map: apps/api/src/schemas/config/.pi-map.md
+- apps/api/src/schemas/project
+  index: apps/api/src/schemas/project/.pi-map.index.md
+  map: apps/api/src/schemas/project/.pi-map.md
+- apps/api/src/schemas/system
+  index: apps/api/src/schemas/system/.pi-map.index.md
+  map: apps/api/src/schemas/system/.pi-map.md
+- apps/api/src/schemas/tool
+  index: apps/api/src/schemas/tool/.pi-map.index.md
+  map: apps/api/src/schemas/tool/.pi-map.md
+- apps/api/src/schemas/user
+  index: apps/api/src/schemas/user/.pi-map.index.md
+  map: apps/api/src/schemas/user/.pi-map.md
+## files
+- __init__.py
+## links
+index: apps/api/src/schemas/.pi-map.index.md
+map: apps/api/src/schemas/.pi-map.md
+## workflows
+- change schemas behavior
+  read: __init__.py
+- explore schemas subdirectories
+  index: apps/api/src/schemas/config/.pi-map.index.md, apps/api/src/schemas/project/.pi-map.index.md, apps/api/src/schemas/system/.pi-map.index.md
+## dirty
+-
@@ -0,0 +1,22 @@
+# apps/api/src/schemas
+dir: apps/api/src/schemas
+
+index: apps/api/src/schemas/.pi-map.index.md
+
+## role
+Defines Pydantic schemas for data validation, serialization, and API request/response models in the FastAPI application.
+## files
+- __init__.py | Empty file with no functionality
+## arch
+Modular schema organization following FastAPI/Pydantic patterns, with empty __init__.py indicating package initialization for future schema modules.
+## tags
+init, empty, functionality
+## symbols
+-
+## workflows
+- change schemas behavior
+  read: __init__.py
+- explore schemas subdirectories
+  index: apps/api/src/schemas/config/.pi-map.index.md, apps/api/src/schemas/project/.pi-map.index.md, apps/api/src/schemas/system/.pi-map.index.md
+## dirty
+-
@@ -0,0 +1,23 @@
+# apps/api/src/schemas/config (index)
+dir: apps/api/src/schemas/config
+
+## role
+Provides Pydantic validation schemas for configuration profile API endpoints, ensuring data integrity for mounts, git URLs, UUIDs, and file paths.
+## parent
+index: apps/api/src/schemas/.pi-map.index.md
+map: apps/api/src/schemas/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- config_profile.py
+## links
+index: apps/api/src/schemas/config/.pi-map.index.md
+map: apps/api/src/schemas/config/.pi-map.md
+## workflows
+- change config behavior
+  read: __init__.py, config_profile.py
+- change config config
+  read: config_profile.py
+## dirty
+-
@@ -0,0 +1,30 @@
+# apps/api/src/schemas/config
+dir: apps/api/src/schemas/config
+
+index: apps/api/src/schemas/config/.pi-map.index.md
+
+## role
+Provides Pydantic validation schemas for configuration profile API endpoints, ensuring data integrity for mounts, git URLs, UUIDs, and file paths.
+## files
+- __init__.py | Re-exports Pydantic schemas for configuration profile operations from a submodule to provide a clean public API. | dep: src.schemas.config.config_profile
+- config_profile.py | Defines Pydantic request/response schemas for config profile API operations with validation for mounts, git URLs, UUIDs, and file paths. | exp: class:GitMountMapping, class:GitMountItem, class:MountItem, class:ConfigProfileCreate, class:ConfigProfileUpdate, class:ConfigProfileIncludeUpdate, class:ConfigProfileResponse, class:DefaultProfilesUpdate, class:ValidateGitUrlRequest, class:ValidateGitUrlResponse, func:_validate_uuid(v: str | None) → str | None, call:uuid.UUID, raise:ValueError | dep: uuid, pydantic, src.api.shared_validators
+## arch
+Simple schema-as-code pattern using Pydantic models with field validators; clean public API via explicit re-exports in `__init__.py`.
+## tags
+profile, config, git, mount, update, validate, response, item
+## symbols
+- GitMountMapping
+- GitMountItem
+- MountItem
+- ConfigProfileCreate
+- ConfigProfileUpdate
+- ConfigProfileIncludeUpdate
+- ConfigProfileResponse
+- DefaultProfilesUpdate
+## workflows
+- change config behavior
+  read: __init__.py, config_profile.py
+- change config config
+  read: config_profile.py
+## dirty
+-
@@ -0,0 +1,23 @@
+# apps/api/src/schemas/project (index)
+dir: apps/api/src/schemas/project
+
+## role
+Provides Pydantic data validation schemas for project-related API endpoints including projects, Git repositories, and SSH keys.
+## parent
+index: apps/api/src/schemas/.pi-map.index.md
+map: apps/api/src/schemas/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- git_repository.py
+- project.py
+- ssh_key.py
+## links
+index: apps/api/src/schemas/project/.pi-map.index.md
+map: apps/api/src/schemas/project/.pi-map.md
+## workflows
+- change project behavior
+  read: __init__.py, git_repository.py, project.py
+## dirty
+-
@@ -0,0 +1,30 @@
+# apps/api/src/schemas/project
+dir: apps/api/src/schemas/project
+
+index: apps/api/src/schemas/project/.pi-map.index.md
+
+## role
+Provides Pydantic data validation schemas for project-related API endpoints including projects, Git repositories, and SSH keys.
+## files
+- __init__.py | Re-exports Pydantic schema classes from submodules to provide a unified public API for the project schemas module | dep: src.schemas.project.git_repository, src.schemas.project.project, src.schemas.project.ssh_key
+- git_repository.py | Defines Pydantic request/response schemas for Git repository operations in an API. | exp: class:GitRepositoryCreate, class:URLParseRequest, class:URLParseResponse, class:GitRepositoryResponse, class:UpdateSSHKeyRequest, class:FileListResponse, class:FileContentResponse, class:BranchesResponse, class:FileUpdateRequest, class:FileUpdateResponse, class:StatusResponse, class:BranchCreateRequest, class:CheckoutRequest, class:CommitRequest, class:CommitResponse, class:FetchResponse, class:PullResponse, class:PushResponse, class:MergeRequest, class:MergeResponse | dep: uuid, datetime, pydantic
+- project.py | Defines Pydantic request/response schemas for project-related API operations. | exp: class:ProjectCreate, class:ProjectUpdate, class:ProjectResponse, class:SetDefaultSSHKeyRequest | dep: uuid, pydantic
+- ssh_key.py | Defines Pydantic schemas for SSH key creation, response, signing, and signature verification in an API. | exp: class:SSHKeyCreate, class:SSHKeyResponse, class:SignPayloadRequest, class:SignatureResponse, class:VerifySignatureRequest, class:VerifySignatureResponse | dep: uuid, datetime, pydantic
+## arch
+Modular schema-per-domain pattern with clean separation of concerns, using Pydantic models for request/response validation and an `__init__.py` facade for unified public API access.
+## tags
+response, request, project, create, update, sshkey, pydantic, schemas
+## symbols
+- GitRepositoryCreate
+- URLParseRequest
+- URLParseResponse
+- GitRepositoryResponse
+- UpdateSSHKeyRequest
+- FileListResponse
+- FileContentResponse
+- BranchesResponse
+## workflows
+- change project behavior
+  read: __init__.py, git_repository.py, project.py
+## dirty
+-
@@ -45,3 +45,91 @@ class GitRepositoryResponse(BaseModel):

 class UpdateSSHKeyRequest(BaseModel):
    ssh_key_id: str | None = None
+
+
+class FileListResponse(BaseModel):
+    path: str
+    branch: str
+    entries: list[dict]
+
+
+class FileContentResponse(BaseModel):
+    path: str
+    branch: str
+    content: str
+    size: int
+    encoding: str
+    language: str | None
+    is_binary: bool
+    last_commit: dict | None
+
+
+class BranchesResponse(BaseModel):
+    branches: list[dict]
+    default_branch: str
+
+
+class FileUpdateRequest(BaseModel):
+    path: str
+    branch: str
+    content: str
+    commit_message: str
+
+
+class FileUpdateResponse(BaseModel):
+    commit_hash: str
+    message: str
+    branch: str
+
+
+class StatusResponse(BaseModel):
+    branch: str
+    modified: list[str]
+    added: list[str]
+    deleted: list[str]
+    untracked: list[str]
+    renamed: list[str]
+    ahead: int
+    behind: int
+
+
+class BranchCreateRequest(BaseModel):
+    name: str
+    base_branch: str = "HEAD"
+
+
+class CheckoutRequest(BaseModel):
+    branch: str
+
+
+class CommitRequest(BaseModel):
+    message: str
+    files: list[str] | None = None
+
+
+class CommitResponse(BaseModel):
+    commit_hash: str
+    message: str
+
+
+class FetchResponse(BaseModel):
+    message: str
+
+
+class PullResponse(BaseModel):
+    message: str
+
+
+class PushResponse(BaseModel):
+    message: str
+
+
+class MergeRequest(BaseModel):
+    source_branch: str
+    target_branch: str | None = None
+    message: str | None = None
+
+
+class MergeResponse(BaseModel):
+    commit_hash: str
+    message: str
@@ -0,0 +1,21 @@
+# apps/api/src/schemas/system (index)
+dir: apps/api/src/schemas/system
+
+## role
+Provides Pydantic schemas for system health monitoring endpoints in the API.
+## parent
+index: apps/api/src/schemas/.pi-map.index.md
+map: apps/api/src/schemas/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- health.py
+## links
+index: apps/api/src/schemas/system/.pi-map.index.md
+map: apps/api/src/schemas/system/.pi-map.md
+## workflows
+- change system behavior
+  read: __init__.py, health.py
+## dirty
+-
@@ -0,0 +1,25 @@
+# apps/api/src/schemas/system
+dir: apps/api/src/schemas/system
+
+index: apps/api/src/schemas/system/.pi-map.index.md
+
+## role
+Provides Pydantic schemas for system health monitoring endpoints in the API.
+## files
+- __init__.py | Re-exports health check schema classes from a submodule to provide a unified interface for the system schemas module. | dep: src.schemas.system.health
+- health.py | Defines Pydantic data models for health check API responses including database, disk, and overall system health status. | exp: class:DatabaseHealth, class:DiskHealth, class:HealthChecks, class:HealthResponse, class:DatabaseHealthResponse | dep: pydantic
+## arch
+Simple submodule pattern with explicit re-exports in __init__.py, using Pydantic models for structured API response validation.
+## tags
+health, database, response, system, disk, check, schemas, init
+## symbols
+- DatabaseHealth
+- DiskHealth
+- HealthChecks
+- HealthResponse
+- DatabaseHealthResponse
+## workflows
+- change system behavior
+  read: __init__.py, health.py
+## dirty
+-
@@ -0,0 +1,22 @@
+# apps/api/src/schemas/tool (index)
+dir: apps/api/src/schemas/tool
+
+## role
+Provides Pydantic data validation schemas for tool-related API operations including tool types and instances.
+## parent
+index: apps/api/src/schemas/.pi-map.index.md
+map: apps/api/src/schemas/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- tool_instance.py
+- tool_type.py
+## links
+index: apps/api/src/schemas/tool/.pi-map.index.md
+map: apps/api/src/schemas/tool/.pi-map.md
+## workflows
+- change tool behavior
+  read: __init__.py, tool_instance.py, tool_type.py
+## dirty
+-
@@ -0,0 +1,27 @@
+# apps/api/src/schemas/tool
+dir: apps/api/src/schemas/tool
+
+index: apps/api/src/schemas/tool/.pi-map.index.md
+
+## role
+Provides Pydantic data validation schemas for tool-related API operations including tool types and instances.
+## files
+- __init__.py | Re-exports tool-related schema classes from submodules to provide a unified import interface for the tool schemas module. | dep: src.schemas.tool.tool_instance, src.schemas.tool.tool_type
+- tool_instance.py | Defines Pydantic request/response schemas for tool instance lifecycle operations (create and start). | exp: class:CreateInstanceRequest, class:StartInstanceRequest | dep: pydantic
+- tool_type.py | Defines Pydantic request/response schemas for creating, updating, and validating tool types with Docker compose/dockerfile/manifest definitions | exp: class:ToolTypeCreate, class:ToolTypeUpdate, class:ToolTypeResponse, class:ToolTypeValidateRequest | dep: uuid, datetime, pydantic, src.api.tool.tool_types_validation
+## arch
+Modular schema organization with submodule-per-entity pattern and unified re-export interface via `__init__.py`, following standard Python package structure for clean API imports.
+## tags
+tool, type, request, instance, schemas, create, pydantic, response
+## symbols
+- CreateInstanceRequest
+- StartInstanceRequest
+- ToolTypeCreate
+- ToolTypeUpdate
+- ToolTypeResponse
+- ToolTypeValidateRequest
+## workflows
+- change tool behavior
+  read: __init__.py, tool_instance.py, tool_type.py
+## dirty
+-
@@ -1,6 +1,10 @@
 """Tool schemas module."""

-from src.schemas.tool.tool_instance import CreateInstanceRequest, StartInstanceRequest
+from src.schemas.tool.tool_instance import (
+    CreateInstanceRequest,
+    CreateWorkspaceInstanceRequest,
+    StartInstanceRequest,
+)
 from src.schemas.tool.tool_type import (
    ToolTypeCreate,
    ToolTypeResponse,
@@ -10,6 +14,7 @@ from src.schemas.tool.tool_type import (

 __all__ = [
    "CreateInstanceRequest",
+    "CreateWorkspaceInstanceRequest",
    "StartInstanceRequest",
    "ToolTypeCreate",
    "ToolTypeResponse",
@@ -13,16 +13,24 @@ class CreateInstanceRequest(BaseModel):
        default=None, description="Optional display name for the instance"
    )
    workspace_id: str | None = Field(
-        default=None, description="UUID of workspace to mount (replaces clone_mode)"
+        default=None, description="UUID of workspace to mount"
    )
-    clone_mode: str = Field(
-        default="mount", description="Repository access mode: 'mount' or 'clone'"
+    config_profile_id: str | None = Field(
+        default=None, description="Optional config profile ID for launch"
    )
-    branch: str | None = Field(
-        default="main", description="Branch to clone (when clone_mode='clone')"
+    ssh_key_ids: list[str] = Field(
+        default_factory=list, description="SSH key IDs to mount into container ~/.ssh"
    )
-    new_branch: str | None = Field(
-        default=None, description="Create a new local branch after cloning"
+
+
+class CreateWorkspaceInstanceRequest(BaseModel):
+    """Request body for creating a tool instance directly on a workspace."""
+
+    model_config = {"extra": "ignore"}
+
+    tool_type_id: str = Field(description="UUID of the tool type to instantiate")
+    display_name: str | None = Field(
+        default=None, description="Optional display name for the instance"
    )
    config_profile_id: str | None = Field(
        default=None, description="Optional config profile ID for launch"
@@ -0,0 +1,24 @@
+# apps/api/src/schemas/user (index)
+dir: apps/api/src/schemas/user
+
+## role
+Provides centralized Pydantic data validation schemas for user-related API requests and responses.
+## parent
+index: apps/api/src/schemas/.pi-map.index.md
+map: apps/api/src/schemas/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- user.py
+- user_config.py
+## links
+index: apps/api/src/schemas/user/.pi-map.index.md
+map: apps/api/src/schemas/user/.pi-map.md
+## workflows
+- change user behavior
+  read: __init__.py, user.py, user_config.py
+- change user config
+  read: user_config.py
+## dirty
+-
@@ -0,0 +1,27 @@
+# apps/api/src/schemas/user
+dir: apps/api/src/schemas/user
+
+index: apps/api/src/schemas/user/.pi-map.index.md
+
+## role
+Provides centralized Pydantic data validation schemas for user-related API requests and responses.
+## files
+- __init__.py | Re-exports user-related Pydantic schemas from submodules to provide a unified public API for the user schemas package. | dep: src.schemas.user.user, src.schemas.user.user_config
+- user.py | Defines Pydantic response and update schemas for user profile data | exp: class:UserProfileResponse, class:UserProfileUpdate | dep: uuid, pydantic
+- user_config.py | Defines Pydantic models for user configuration data transfer objects (response and update schemas). | exp: class:UserConfigResponse, class:UserConfigUpdate | dep: pydantic
+## arch
+Modular package pattern with submodule separation of concerns (user profile vs. user config) and unified public API via `__init__.py` re-exports.
+## tags
+user, schemas, response, update, config, pydantic, profile, src
+## symbols
+- UserProfileResponse
+- UserProfileUpdate
+- UserConfigResponse
+- UserConfigUpdate
+## workflows
+- change user behavior
+  read: __init__.py, user.py, user_config.py
+- change user config
+  read: user_config.py
+## dirty
+-
@@ -0,0 +1,21 @@
+# apps/api/src/scripts (index)
+dir: apps/api/src/scripts
+
+## role
+Provides utility scripts for administrative and setup tasks for the API application.
+## parent
+index: apps/api/src/.pi-map.index.md
+map: apps/api/src/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- seed.py
+## links
+index: apps/api/src/scripts/.pi-map.index.md
+map: apps/api/src/scripts/.pi-map.md
+## workflows
+- change scripts behavior
+  read: __init__.py, seed.py
+## dirty
+-
@@ -0,0 +1,28 @@
+# apps/api/src/scripts
+dir: apps/api/src/scripts
+
+index: apps/api/src/scripts/.pi-map.index.md
+
+## role
+Provides utility scripts for administrative and setup tasks for the API application.
+## files
+- __init__.py | Marks the directory as a Python package and provides a docstring describing it as utility scripts for the API package.
+- seed.py | Seeds a development user into the database using SQLAlchemy async operations, with idempotency check to avoid duplicates. | exp: func:build_seed_user() → Mapping[str, str | None], func:seed_database(session: AsyncSession) → User, call:build_seed_user, call:session.scalar, call:select(User).where, call:User, call:session.add, call:session.commit, call:session.refresh, func:run() → None, call:SessionLocal, call:seed_database, call:print, call:str, func:main() → None, call:asyncio.run, call:run | dep: collections.abc, sqlalchemy, sqlalchemy.ext.asyncio, src.database, src.models.user, asyncio
+## arch
+Simple procedural scripts using async SQLAlchemy for database operations, with idempotency guards for safe re-runs.
+## tags
+seed, user, database, sqlalchemy, package, init, call:build, call:session.scalar
+## symbols
+- build_seed_user
+- seed_database
+- run
+- main
+- call:build_seed_user
+- call:session.scalar
+- call:select(User).where
+- call:User
+## workflows
+- change scripts behavior
+  read: __init__.py, seed.py
+## dirty
+-
@@ -0,0 +1,21 @@
+# apps/api/src/seeds (index)
+dir: apps/api/src/seeds
+
+## role
+Provides database seeding utilities for initializing built-in tool types in the API application.
+## parent
+index: apps/api/src/.pi-map.index.md
+map: apps/api/src/.pi-map.md
+## children
+-
+## files
+- __init__.py
+- builtin_tool_types.py
+## links
+index: apps/api/src/seeds/.pi-map.index.md
+map: apps/api/src/seeds/.pi-map.md
+## workflows
+- change seeds behavior
+  read: __init__.py, builtin_tool_types.py
+## dirty
+-
@@ -0,0 +1,28 @@
+# apps/api/src/seeds
+dir: apps/api/src/seeds
+
+index: apps/api/src/seeds/.pi-map.index.md
+
+## role
+Provides database seeding utilities for initializing built-in tool types in the API application.
+## files
+- __init__.py | Marks the directory as a Python package for database seeding utilities.
+- builtin_tool_types.py | Seeds built-in Docker Compose-based tool types (VS Code Server, Jupyter Notebook, OpenCode) into a database with idempotent create-or-update logic. | exp: func:_table_exists(session, table_name: str) → bool, call:session.execute, call:text, call:result.scalar, func:seed_builtin_tool_types(), call:SessionLocal, call:_table_exists, call:logger.warning, call:session.scalar, call:select(ToolType).where, call:ToolType, call:tool_data.get, call:session.add, call:logger.info, call:session.commit | dep: logging, sqlalchemy, src.database, src.models
+## arch
+Simple procedural seeding scripts with idempotent create-or-update logic using direct database operations, organized as a Python package with one seed module per entity type.
+## tags
+tool, types, table, exists, builtin, call:tool, database, init
+## symbols
+- _table_exists
+- seed_builtin_tool_types
+- call:session.execute
+- call:text
+- call:result.scalar
+- call:SessionLocal
+- call:_table_exists
+- call:logger.warning
+## workflows
+- change seeds behavior
+  read: __init__.py, builtin_tool_types.py
+## dirty
+-
@@ -0,0 +1,42 @@
+# apps/api/src/services (index)
+dir: apps/api/src/services
+
+## role
+Initializes the services directory as a Python package for business logic modules.
+## parent
+index: apps/api/src/.pi-map.index.md
+map: apps/api/src/.pi-map.md
+## children
+- apps/api/src/services/config
+  index: apps/api/src/services/config/.pi-map.index.md
+  map: apps/api/src/services/config/.pi-map.md
+- apps/api/src/services/docker
+  index: apps/api/src/services/docker/.pi-map.index.md
+  map: apps/api/src/services/docker/.pi-map.md
+- apps/api/src/services/git
+  index: apps/api/src/services/git/.pi-map.index.md
+  map: apps/api/src/services/git/.pi-map.md
+- apps/api/src/services/instance
+  index: apps/api/src/services/instance/.pi-map.index.md
+  map: apps/api/src/services/instance/.pi-map.md
+- apps/api/src/services/shared
+  index: apps/api/src/services/shared/.pi-map.index.md
+  map: apps/api/src/services/shared/.pi-map.md
+- apps/api/src/services/terminal
+  index: apps/api/src/services/terminal/.pi-map.index.md
+  map: apps/api/src/services/terminal/.pi-map.md
+- apps/api/src/services/tool
+  index: apps/api/src/services/tool/.pi-map.index.md
+  map: apps/api/src/services/tool/.pi-map.md
+## files
+- __init__.py
+## links
+index: apps/api/src/services/.pi-map.index.md
+map: apps/api/src/services/.pi-map.md
+## workflows
+- change services behavior
+  read: __init__.py
+- explore services subdirectories
+  index: apps/api/src/services/config/.pi-map.index.md, apps/api/src/services/docker/.pi-map.index.md, apps/api/src/services/git/.pi-map.index.md
+## dirty
+-
@@ -0,0 +1,22 @@
+# apps/api/src/services
+dir: apps/api/src/services
+
+index: apps/api/src/services/.pi-map.index.md
+
+## role
+Initializes the services directory as a Python package for business logic modules.
+## files
+- __init__.py | Empty file with no functionality
+## arch
+Standard Python package structure using empty __init__.py for namespace declaration.
+## tags
+init, empty, functionality
+## symbols
+-
+## workflows
+- change services behavior
+  read: __init__.py
+- explore services subdirectories
+  index: apps/api/src/services/config/.pi-map.index.md, apps/api/src/services/docker/.pi-map.index.md, apps/api/src/services/git/.pi-map.index.md
+## dirty
+-
@@ -172,10 +172,19 @@ def compile_dockerfile(manifest: dict) -> str:
        lines.append(f"ENV HOME={home}")
        lines.append(f"ENV USER={name}")
        lines.append("")
-        # Ensure home directory exists and is writable by the user
+        # Ensure home directory exists and is writable by the user.
+        # Recursively chown so any files copied from /etc/skel by useradd -m
+        # (e.g. .bashrc, .config) are owned by the container user.
        lines.append(
-            f"RUN mkdir -p {home} && chown {name}:{name} {home} && chmod 755 {home}"
+            f"RUN mkdir -p {home} && chown -R {name}:{name} {home} && chmod 755 {home}"
        )
+        # Pre-create common config directories so apps like ranger can write
+        # their configs on first run without permission errors.
+        common_dirs = [".config", ".local/share", ".cache"]
+        for d in common_dirs:
+            lines.append(
+                f"RUN mkdir -p {home}/{d} && chown -R {name}:{name} {home}/{d}"
+            )
        lines.append("")

        # Configure passwordless sudo so startup scripts can fix permissions
--- a/Show More
+++ b/Show More