fix: resolve four frontend/backend issues

- Fix ProjectsPage tests by wrapping renders in MemoryRouter (9 passing)
- Improve session auto-naming to 'project / repo / tool' format
- Add missing /users/me/sessions endpoint for sidebar session loading
- Handle git history 500s: catch RuntimeError in endpoints, graceful empty repo handling
- Add git status badge and discard-changes button to FileEditor toolbar

Quality gates: tsc pass, build pass, Python syntax pass

.atl/.skill-registry.cache.json

@@ -1,3 +0,0 @@
-{
-  "fingerprint": "639c16d45210921c3c8ece071ef18bbe0c426ea2"
-}

.atl/skill-registry.md

@@ -1,33 +0,0 @@
-# Skill Registry — workspace
-
-<!-- Auto-generated by gentle-pi extensions/skill-registry.ts. Run /skill-registry:refresh to regenerate. -->
-
-Last updated: 2026-06-05
-
-## Sources scanned
-
-- .opencode/skills
-- .claude/skills
-
-## Contract
-
-**Delegator use only.** This registry is an index, not a summary. Any agent that launches subagents reads it to select relevant skills, then passes exact `SKILL.md` paths for the subagent to read before work.
-
-`SKILL.md` remains the source of truth. Do not inject generated summaries or compact rules by default; pass paths so subagents load the full runtime contract and preserve author intent.
-
-## Skills
-
-| Skill | Trigger / description | Scope | Path |
-| --- | --- | --- | --- |
-| `openspec-apply-change` | Implement tasks from an OpenSpec change. Use when the user wants to start implementing, continue implementation, or work through tasks. | project | `/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
-
-1. Match task context and target files against the `Trigger / description` column.
-2. Pass only the matching `Path` values to the subagent under `## Skills to load before work`.
-3. Instruct the subagent to read those exact `SKILL.md` files before reading, writing, reviewing, testing, or creating artifacts.
-4. If no matching skill exists, proceed without project skill injection and report `skill_resolution: none`.

.claude/.pi-map.index.md

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

.claude/.pi-map.md

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

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

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

.claude/skills/.pi-map.md

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

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

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

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

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

.claude/skills/sift-backlog/SKILL.md

@@ -1,195 +0,0 @@
----
-name: sift-backlog
-description: 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.
----
-
-# Sift Backlog
-
-Triage backlog tasks: prioritize, group into plans, set dependencies, and activate.
-
-## Overview
-
-1. List backlog tasks (`sf task backlog`)
-2. Clarify and enrich each task (titles, descriptions)
-3. Identify groupings and create draft plans
-4. Add tasks to plans and set dependencies
-5. Activate plans
-6. Set task status to open
-
-## Workflow
-
-### Step 1: List Backlog Tasks
-
-```bash
-sf task backlog
-```
-
-### Step 2: Clarify and Enrich Tasks
-
-Backlog tasks often have only a brief title with no description. Before organizing, ensure each task is well-defined.
-
-**For each task, evaluate:**
-
-- Is the title clear and actionable?
-- Is there a description? Check with `sf task describe <task-id> --show`
-- Is the scope unambiguous?
-
-**If the title is unclear**, update it:
-
-```bash
-sf update <task-id> --title "Clear, actionable title"
-```
-
-**Add a description** with context, scope, and acceptance criteria:
-
-```bash
-sf task describe <task-id> --content "Description with:
-- What needs to be done
-- Why it matters
-- Acceptance criteria
-- Any relevant context"
-```
-
-**Use your best judgment** to interpret tasks and make reasonable decisions about scope, grouping, and priority. You have context about the codebase, project patterns, and typical development practices—leverage this knowledge rather than deferring to the user for routine decisions.
-
-**Only ask the user for clarity when absolutely necessary:**
-
-- The task is fundamentally ambiguous (multiple mutually exclusive interpretations)
-- Critical business logic or user-facing behavior that could go wrong in meaningful ways
-- External dependencies or integrations you cannot verify
-
-**Do NOT ask about:**
-
-- Implementation details you can reasonably infer
-- Priority or grouping decisions—use your judgment
-- Standard development practices (testing, code style, etc.)
-- Tasks where a reasonable interpretation exists
-
-### Step 3: Create Draft Plans
-
-Group related tasks into plans using your best judgment. Plans start as drafts (tasks won't be dispatched until activated).
-
-**Grouping guidance:**
-
-- Group tasks that share a common theme, feature area, or goal
-- Consider technical dependencies when grouping (tasks that touch the same files/modules)
-- Separate unrelated work into distinct plans for parallel execution
-- Don't over-group—if tasks are truly independent, separate plans enable better parallelism
-- Don't under-group—related tasks benefit from shared context and coordinated execution
-
-```bash
-sf plan create --title "Plan Name"
-```
-
-**Example:**
-
-```bash
-sf plan create --title "Authentication Improvements"
-# Output: Created plan el-abc123
-```
-
-### Step 4: Add Tasks to Plans
-
-```bash
-sf plan add-task <plan-id> <task-id>
-```
-
-**Example:**
-
-```bash
-sf plan add-task el-abc123 el-task1
-sf plan add-task el-abc123 el-task2
-```
-
-### Step 5: Set Dependencies Between Tasks
-
-Use `blocks` dependency when one task must complete before another can start.
-
-```bash
-sf dependency add <blocked-id> <blocker-id> --type blocks
-```
-
-**Semantics:** The first ID is blocked BY the second ID. The blocker must complete first.
-
-**Example:** Task 2 can't start until Task 1 completes:
-
-```bash
-sf dependency add el-task2 el-task1 --type blocks
-```
-
-### Step 6: Update Priorities
-
-Set priorities based on your assessment of impact, urgency, and dependencies. Use your judgment—you don't need user confirmation for routine prioritization.
-
-**Priority guidance:**
-
-- **Critical (1):** Blocking issues, security vulnerabilities, production bugs
-- **High (2):** Important features with deadlines, significant user impact
-- **Medium (3):** Standard feature work, most tasks default here
-- **Low (4):** Nice-to-haves, minor improvements, tech debt
-- **Minimal (5):** Backlog cleanup, documentation, exploratory work
-
-```bash
-sf update <task-id> --priority <1-5>
-```
-
-| Value | Level    |
-| ----- | -------- |
-| 1     | Critical |
-| 2     | High     |
-| 3     | Medium   |
-| 4     | Low      |
-| 5     | Minimal  |
-
-### Step 7: Activate Plans
-
-Once tasks are organized with dependencies set, activate plans to enable dispatch.
-
-```bash
-sf plan activate <plan-id>
-```
-
-### Step 8: Set Task Status to Open
-
-Move tasks from backlog to open so they become ready for work.
-
-```bash
-sf update <id> --status open
-```
-
-## Other Actions
-
-**Close obsolete tasks:**
-
-```bash
-sf task close <id> --reason "Won't do: <reason>"
-```
-
-**Defer tasks:**
-
-```bash
-sf task defer <id> --until <date>
-```
-
-**View existing plans:**
-
-```bash
-sf plan list
-```
-
-**View tasks in a plan:**
-
-```bash
-sf plan tasks <plan-id>
-```
-
-## Tips
-
-- **Use your best judgment** for grouping, prioritization, and task interpretation—don't defer routine decisions to the user
-- **Only escalate to the user** when ambiguity is fundamental and could lead to wasted work (mutually exclusive interpretations, critical business decisions)
-- Make reasonable inferences about implementation details, scope, and priority based on codebase context
-- Create plans before setting dependencies to avoid dispatch race conditions
-- Always activate plans after dependencies are set
-- Focus on oldest backlog items first (sorted by creation date)
-- Every task should have a clear title and description before activation
-- When uncertain about a minor detail, make a reasonable choice and document it in the task description—workers can ask if needed

.gitignore

@@ -17,7 +17,6 @@ __pycache__/
 *.so
 .python-version
 .venv/
-.venv-test/
 venv/
 env/
 .pytest_cache/
@@ -49,12 +48,8 @@ apps/web/dist/
 # OS
 .DS_Store
 Thumbs.db
-/.stoneforge/.worktrees/
-# Pi / agent cache
-.pi/
+
+# Local runtime state
 .atl/
-.sisyphus/
-.pi-lens/
-minerv3/
-.cache/
-openspec-audit-report.md
+.pi/
+swap-pane

.opencode/.pi-map.index.md

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

.opencode/.pi-map.md

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

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

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

.opencode/commands/.pi-map.md

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

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

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

.opencode/skills/.pi-map.md

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

.pi-map.index.md

@@ -1,79 +0,0 @@
-# . (index)
-dir: .
-
-## Project Map Protocol
-
-1. Read this protocol and the root `.pi-map.index.md` first.
-2. Use `index:` / `map:` references to open relevant directory indexes and maps.
-3. Load indexes before rich maps during task-start navigation.
-4. Read the local rich map and actual source before editing.
-5. Treat non-empty `## dirty` sections in either artifact as stale.
-6. If source and generated artifacts disagree, trust source.
-7. If map and index disagree, trust neither blindly; verify from source and regenerate the pair.
-8. After editing source, run `project_map_patch` for each changed file.
-9. Before broad architectural claims or final handoff, run `project_map_validate` when freshness matters.
-
-Trust boundary: index routes, map orients, source decides.
-
-## role
-A self-hosted web platform for managing projects, git repositories, and development tools with OAuth2 authentication, built as a Dockerized multi-service application.
-## parent
--
-## children
-- .atl
-  index: .atl/.pi-map.index.md
-  map: .atl/.pi-map.md
-- .claude
-  index: .claude/.pi-map.index.md
-  map: .claude/.pi-map.md
-- .opencode
-  index: .opencode/.pi-map.index.md
-  map: .opencode/.pi-map.md
-- .pi
-  index: .pi/.pi-map.index.md
-  map: .pi/.pi-map.md
-- .sisyphus
-  index: .sisyphus/.pi-map.index.md
-  map: .sisyphus/.pi-map.md
-- .stoneforge
-  index: .stoneforge/.pi-map.index.md
-  map: .stoneforge/.pi-map.md
-- apps
-  index: apps/.pi-map.index.md
-  map: apps/.pi-map.md
-- docs
-  index: docs/.pi-map.index.md
-  map: docs/.pi-map.md
-- e2e
-  index: e2e/.pi-map.index.md
-  map: e2e/.pi-map.md
-- openspec
-  index: openspec/.pi-map.index.md
-  map: openspec/.pi-map.md
-- scripts
-  index: scripts/.pi-map.index.md
-  map: scripts/.pi-map.md
-- tool-images
-  index: tool-images/.pi-map.index.md
-  map: tool-images/.pi-map.md
-## files
-- .env.example
-- .gitignore
-- AGENTS.md
-- CHANGELOG.md
-- Makefile
-- README.md
-- docker-compose.traefik.yml
-- docker-compose.yml
-- progress.md
-- swap-pane
-- ui-audit-spacing-typography.md
-- ui-rework-foundations-apply.md
-- ui-rework-pass2-apply.md
-## links
-index: ./.pi-map.index.md
-map: ./.pi-map.md
-## workflows
--
-## dirty
--

.pi-map.md

@@ -1,45 +0,0 @@
-# .
-dir: .
-
-index: ./.pi-map.index.md
-
-## Project Map Protocol
-
-1. Read this protocol and the root `.pi-map.index.md` first.
-2. Use `index:` / `map:` references to open relevant directory indexes and maps.
-3. Load indexes before rich maps during task-start navigation.
-4. Read the local rich map and actual source before editing.
-5. Treat non-empty `## dirty` sections in either artifact as stale.
-6. If source and generated artifacts disagree, trust source.
-7. If map and index disagree, trust neither blindly; verify from source and regenerate the pair.
-8. After editing source, run `project_map_patch` for each changed file.
-9. Before broad architectural claims or final handoff, run `project_map_validate` when freshness matters.
-
-Trust boundary: index routes, map orients, source decides.
-
-## role
-A self-hosted web platform for managing projects, git repositories, and development tools with OAuth2 authentication, built as a Dockerized multi-service application.
-## files
-- .env.example | Template environment configuration file defining all required and optional environment variables for a multi-service application stack
-- .gitignore | Specifies patterns for files and directories that Git should ignore in this project. | dep: git
-- AGENTS.md | Defines agent behavior rules, workflow procedures, and project conventions for AI agents working on an OpenSpec-driven codebase. | dep: OpenSpec, git, superpowers workflow system, conventional commits
-- CHANGELOG.md | Documents version history and notable changes to a project management and Git repository application
-- Makefile | Provides standard development commands for managing a Docker Compose-based multi-service application (API, web, Postgres, Redis) with testing, migration, linting, and build automation. | dep: docker compose, alembic, pytest, ruff, mypy, playwright, npm/node
-- 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
-- docker-compose.traefik.yml | Deploys a multi-service web application stack (frontend, API, PostgreSQL, Redis) behind an existing Traefik reverse proxy with automatic HTTPS | dep: Docker, Docker Compose, Traefik, PostgreSQL, Redis, Authentik
-- docker-compose.yml | Defines a multi-container Docker application with PostgreSQL, Redis, API backend, and web frontend services for a "headquarter" application. | dep: Docker Compose, PostgreSQL 15, Redis 7, Python/FastAPI (implied by asyncpg), Vite/Node.js (implied by web build), Alpine Linux
-- progress.md | Documents the completed phases and remaining work of a backend-frontend code refactoring project involving modularization, subpackage extraction, and file reorganization.
-- swap-pane | Swaps two tmux panes between windows, preserving active pane state and layout | dep: tmux
-- ui-audit-spacing-typography.md | Documents a comprehensive UI audit of spacing, typography, and visual rhythm issues in a React web application, identifying missing CSS classes, unstyled mobile components, inconsistent design tokens, and layout bugs across component and stylesheet files. | dep: React/TSX components, CSS modules/stylesheets, CSS custom properties (tokens), mobile-specific components, design system tokens
-- ui-rework-foundations-apply.md | Documents the implementation of Pass 1 (Foundations) of a web UI spacing/typography/visual-rhythm rework, including token expansion, primitive CSS classes, component updates, and validation results. | dep: CSS design tokens, React/TSX components, OpenSpec documentation system, git/SSH, npm build toolchain
-- ui-rework-pass2-apply.md | Documents a completed web UI refactoring pass that converted inline styles to token-based utility classes, unified form patterns, and added component utilities across multiple React components. | dep: React, CSS custom properties, OpenSpec, Git, npm, TypeScript, ESLint
-## arch
-Full-stack monolithic architecture with React frontend, API backend, PostgreSQL and Redis services, containerized via Docker Compose, using Traefik for reverse proxy/HTTPS, and following a token-based design system for UI consistency.
-## tags
-docker, application, git, web, react, ui, documents, rework
-## symbols
--
-## workflows
--
-## dirty
--

.pi/settings.json

@@ -1 +0,0 @@
-{}

.sisyphus/run-continuation/ses_1da2608b1ffergOzow3NQt1mGr.json

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

.stoneforge/.dashboard-opened

@@ -1,2 +0,0 @@
-262629
-1779624255076

.stoneforge/.gitignore

@@ -1,6 +0,0 @@
-# Runtime data
-*.db
-*.db-journal
-*.db-wal
-*.db-shm
-daemon-state.json

.stoneforge/.pi-map.index.md

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

.stoneforge/.pi-map.md

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

.stoneforge/config.yaml

@@ -1,20 +0,0 @@
-# Stoneforge Configuration
-
-database: stoneforge.db
-sync:
-  auto_export: true
-  elements_file: elements.jsonl
-  dependencies_file: dependencies.jsonl
-playbooks:
-  paths:
-    - playbooks
-identity:
-  mode: soft
-merge:
-  auto_merge: true
-  target_branch: null
-  require_approval: false
-workflow:
-  preset: auto
-agents:
-  permission_model: unrestricted

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

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

.stoneforge/sync/.pi-map.md

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

.stoneforge/sync/dependencies.jsonl

@@ -1,43 +0,0 @@
-{"blockedId":"el-1of","blockerId":"el-258","type":"parent-child","createdAt":"2026-05-24T09:44:58.759Z","createdBy":"el-2jua"}
-{"blockedId":"el-5fe","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:40.892Z","createdBy":"el-2jua"}
-{"blockedId":"el-1nj","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.010Z","createdBy":"el-2jua"}
-{"blockedId":"el-1bn","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.127Z","createdBy":"el-2jua"}
-{"blockedId":"el-4hr","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.244Z","createdBy":"el-2jua"}
-{"blockedId":"el-62c","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.372Z","createdBy":"el-2jua"}
-{"blockedId":"el-5z8","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.490Z","createdBy":"el-2jua"}
-{"blockedId":"el-1t7","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.607Z","createdBy":"el-2jua"}
-{"blockedId":"el-5j5","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.726Z","createdBy":"el-2jua"}
-{"blockedId":"el-2xl","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.844Z","createdBy":"el-2jua"}
-{"blockedId":"el-4bc","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:41.959Z","createdBy":"el-2jua"}
-{"blockedId":"el-107","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.074Z","createdBy":"el-2jua"}
-{"blockedId":"el-32e","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.195Z","createdBy":"el-2jua"}
-{"blockedId":"el-3ou","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.311Z","createdBy":"el-2jua"}
-{"blockedId":"el-14w","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.425Z","createdBy":"el-2jua"}
-{"blockedId":"el-1ou","blockerId":"el-20no","type":"parent-child","createdAt":"2026-05-24T12:44:42.541Z","createdBy":"el-2jua"}
-{"blockedId":"el-1nj","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.651Z","createdBy":"el-2jua"}
-{"blockedId":"el-1bn","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.761Z","createdBy":"el-2jua"}
-{"blockedId":"el-4hr","blockerId":"el-5fe","type":"blocks","createdAt":"2026-05-24T12:44:42.868Z","createdBy":"el-2jua"}
-{"blockedId":"el-62c","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:42.979Z","createdBy":"el-2jua"}
-{"blockedId":"el-62c","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:43.092Z","createdBy":"el-2jua"}
-{"blockedId":"el-5z8","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:43.205Z","createdBy":"el-2jua"}
-{"blockedId":"el-5z8","blockerId":"el-4hr","type":"blocks","createdAt":"2026-05-24T12:44:43.313Z","createdBy":"el-2jua"}
-{"blockedId":"el-1t7","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:43.422Z","createdBy":"el-2jua"}
-{"blockedId":"el-1t7","blockerId":"el-4hr","type":"blocks","createdAt":"2026-05-24T12:44:43.529Z","createdBy":"el-2jua"}
-{"blockedId":"el-1t7","blockerId":"el-62c","type":"blocks","createdAt":"2026-05-24T12:44:43.647Z","createdBy":"el-2jua"}
-{"blockedId":"el-5j5","blockerId":"el-1t7","type":"blocks","createdAt":"2026-05-24T12:44:43.758Z","createdBy":"el-2jua"}
-{"blockedId":"el-2xl","blockerId":"el-1t7","type":"blocks","createdAt":"2026-05-24T12:44:43.876Z","createdBy":"el-2jua"}
-{"blockedId":"el-4bc","blockerId":"el-1nj","type":"blocks","createdAt":"2026-05-24T12:44:43.987Z","createdBy":"el-2jua"}
-{"blockedId":"el-4bc","blockerId":"el-1bn","type":"blocks","createdAt":"2026-05-24T12:44:44.096Z","createdBy":"el-2jua"}
-{"blockedId":"el-4bc","blockerId":"el-62c","type":"blocks","createdAt":"2026-05-24T12:44:44.208Z","createdBy":"el-2jua"}
-{"blockedId":"el-107","blockerId":"el-5z8","type":"blocks","createdAt":"2026-05-24T12:44:44.319Z","createdBy":"el-2jua"}
-{"blockedId":"el-32e","blockerId":"el-5j5","type":"blocks","createdAt":"2026-05-24T12:44:44.429Z","createdBy":"el-2jua"}
-{"blockedId":"el-32e","blockerId":"el-2xl","type":"blocks","createdAt":"2026-05-24T12:44:44.539Z","createdBy":"el-2jua"}
-{"blockedId":"el-3ou","blockerId":"el-4bc","type":"blocks","createdAt":"2026-05-24T12:44:44.650Z","createdBy":"el-2jua"}
-{"blockedId":"el-3ou","blockerId":"el-107","type":"blocks","createdAt":"2026-05-24T12:44:44.761Z","createdBy":"el-2jua"}
-{"blockedId":"el-14w","blockerId":"el-32e","type":"blocks","createdAt":"2026-05-24T12:44:44.873Z","createdBy":"el-2jua"}
-{"blockedId":"el-1ou","blockerId":"el-3ou","type":"blocks","createdAt":"2026-05-24T12:44:44.987Z","createdBy":"el-2jua"}
-{"blockedId":"el-1ou","blockerId":"el-14w","type":"blocks","createdAt":"2026-05-24T12:44:45.107Z","createdBy":"el-2jua"}
-{"blockedId":"el-375","blockerId":"el-26p","type":"replies-to","createdAt":"2026-05-24T13:21:42.486Z","createdBy":"el-2i1s"}
-{"blockedId":"el-3n4","blockerId":"el-31p","type":"replies-to","createdAt":"2026-05-24T13:21:46.044Z","createdBy":"el-13ju"}
-{"blockedId":"el-3jer","blockerId":"el-1xx","type":"replies-to","createdAt":"2026-05-24T13:24:47.580Z","createdBy":"el-4350"}
-{"blockedId":"el-1afv","blockerId":"el-1ozw","type":"replies-to","createdAt":"2026-05-24T13:32:42.658Z","createdBy":"el-51a8"}

AGENTS.md

@@ -4,10 +4,6 @@
 
 OpenSpec is the source of truth. Superpowers is the default workflow. Keep changes small, scoped, and verified.
 
-## Communication
-
-All agent output, code comments, commit messages, documentation, and artifacts must be in **English** unless the user explicitly requests another language.
-
 ## Priority order
 
 1. Current user instruction
@@ -75,7 +71,6 @@ Do not:
 * Introduce new dependencies without clear justification.
 * Treat existing code as more authoritative than OpenSpec for intended behavior.
 * Decide product behavior silently when the spec is unclear.
-* Run `docker compose` commands (build, up, down, etc.) without explicit user approval and proper isolation (e.g., feature branches, separate worktrees, or staged rollouts). Docker Compose operations are deployment-level changes that can affect running services, shared volumes, and network state. Always ask first.
 
 If scope must change, propose an OpenSpec update first.
 
@@ -92,31 +87,6 @@ Do not claim completion without verification evidence.
 
 ## Git workflow
 
-### Branching strategy
-
-For every spec change or new functionality:
-
-1. Create a new branch from `dev` with a proper prefix:
-   - `feat/` for new features (e.g., `feat/tool-workshop`)
-   - `fix/` for bug fixes (e.g., `fix/terminal-tty`)
-   - `refactor/` for refactors (e.g., `refactor/api-cleanup`)
-   - `docs/` for documentation (e.g., `docs/api-guide`)
-   - `chore/` for maintenance (e.g., `chore/update-deps`)
-2. Branch name should reference the OpenSpec change name when applicable.
-3. Do not commit directly to `main` or `dev`.
-
-### Completion and merge
-
-When implementation is complete and verified:
-
-1. Ensure all tests pass and quality gates are met.
-2. Stage all changes with `git add -A`.
-3. Create a commit with a proper conventional commit message (see below).
-4. Switch to `dev`: `git checkout dev`.
-5. Merge the feature branch: `git merge --no-ff <branch-name>`.
-6. Push to remote: `git push origin dev`.
-7. Delete the local feature branch if desired: `git branch -d <branch-name>`.
-
 ### Auto-commit on spec completion
 
 When an OpenSpec change is fully implemented and all tasks are complete:

CHANGELOG.md

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

apps/.pi-map.index.md

@@ -1,23 +0,0 @@
-# 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
--

apps/.pi-map.md

@@ -1,18 +0,0 @@
-# apps
-dir: apps
-
-index: apps/.pi-map.index.md
-
-## role
-Contains the main application entry points and executable modules for the project.
-## files
-## arch
-Modular application structure with separate deployable units, likely following microservices or multi-app monorepo pattern with shared infrastructure.
-## tags
--
-## symbols
--
-## workflows
--
-## dirty
--

apps/api/.dockerignore

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

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

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

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

@@ -1,39 +0,0 @@
-# apps/api (index)
-dir: apps/api
-
-## role
-FastAPI-based backend API service for managing projects, git repositories, and development tools in a self-hosted development platform.
-## 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/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
--

apps/api/.pi-map.md

@@ -1,25 +0,0 @@
-# apps/api
-dir: apps/api
-
-index: apps/api/.pi-map.index.md
-
-## role
-FastAPI-based backend API service for managing projects, git repositories, and development tools in a self-hosted development platform.
-## files
-- .dockerignore | Specifies files and directories to exclude from Docker build context to reduce image size and improve build performance. | dep: Docker
-- Dockerfile | Multi-stage Docker image for a Python web application with Docker-in-Docker capabilities, database waiting, and Cloudflare tunnel support | dep: python:3.11-slim, gcc, libpq-dev, docker-ce-cli, docker-compose-plugin, cloudflared, uvicorn, pyproject.toml dependencies
-- README.md | README documentation for Headquarter API, a self-hosted FastAPI backend for managing projects, git repositories, and development tools. | dep: FastAPI, SQLAlchemy, PostgreSQL, asyncpg, Alembic, Docker, Docker Compose, Authentik, uvicorn, pytest, ruff, mypy
-- alembic.ini | Configuration file for Alembic database migration tool specifying script location, database connection URL, and logging settings | dep: alembic, sqlalchemy, asyncpg, postgresql
-- pyproject.toml | Defines Python project configuration, dependencies, and tool settings for a FastAPI-based backend API service | dep: fastapi, uvicorn, sqlalchemy, asyncpg, alembic, pydantic, pydantic-settings, python-multipart, httpx, structlog, cryptography, pytest, pytest-asyncio, mypy, ruff, aiosqlite
-- uv.lock | Lock file generated by uv package manager that records exact dependency versions, hashes, and download URLs for reproducible Python environment installation | dep: uv, PyPI, python
-- wait-for-db.sh | Waits for a PostgreSQL database to become available before executing the provided command | dep: nc (netcat), sh, sleep
-## arch
-Modern Python backend with FastAPI, SQLAlchemy/ORM with Alembic migrations, uv for dependency management, multi-stage Docker containerization with Docker-in-Docker support, and PostgreSQL database connectivity.
-## tags
-docker, alembic, python, database, fastapi, uvicorn, pyproject, readme
-## symbols
--
-## workflows
--
-## dirty
--

apps/api/Dockerfile

@@ -27,7 +27,6 @@ WORKDIR /app
 RUN apt-get update && apt-get install -y --no-install-recommends \
     libpq5 \
     git \
-    openssh-client \
     netcat-openbsd \
     ca-certificates \
     curl \
@@ -50,8 +49,8 @@ ENV PATH=/root/.local/bin:$PATH
 # Copy application code
 COPY --chown=appuser:appgroup . .
 
-# Create directories for repo, instance, and workspace storage
-RUN mkdir -p /data/repos /data/instances /data/working-copies && chown -R appuser:appgroup /data
+# Create directories for repo and instance storage
+RUN mkdir -p /data/repos /data/instances && chown -R appuser:appgroup /data
 
 # Copy wait-for-db script
 COPY wait-for-db.sh /usr/local/bin/wait-for-db.sh

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

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

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

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

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

@@ -1,73 +0,0 @@
-# apps/api/alembic/versions (index)
-dir: apps/api/alembic/versions
-
-## role
-Manages database schema evolution and version control for the API application using Alembic migration scripts.
-## 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
-- 2026_06_13_make_clone_mode_nullable.py
-- 2026_06_14_104415_add_tool_type_home_directory.py
-- 2026_06_14_182955_fix_pi_agent_home_directory_mount.py
-- 2026_06_15_090500_remove_pi_agent_explicit_repo_mount.py
-- 398082499c30_add_tool_config_fields.py
-- 6fc7bfcf199f_merge_remove_is_builtin_and_add_config_.py
-- 86cec91fdb00_merge_profile_resolver_and_workspaces_.py
-- 8c6d1dbd4798_remove_pi_config_and_state_mounts_from_.py
-- 8ed7dd80973d_create_config_folders_table.py
-- af8512103d67_add_tool_type_fields.py
-- f3d2dc90ba3a_merge_single_interface_and_clone_mode.py
-- fc8f1a20cbf6_merge_home_directory_and_pi_agent_mount_.py
-## links
-index: apps/api/alembic/versions/.pi-map.index.md
-map: apps/api/alembic/versions/.pi-map.md
-## workflows
-- change versions behavior
-  read: 0001_initial_schema.py, 0002_refresh_tokens.py, 0003_user_configs.py
-- change versions CLI
-  read: 2026_05_24_220141_add_startup_command.py, 2026_05_29_remove_lsio_command_override.py
-- change versions config
-  read: 0003_user_configs.py, 0009_tool_configs.py, 0013_add_config_profiles.py
-## dirty
--

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

@@ -1,80 +0,0 @@
-# apps/api/alembic/versions
-dir: apps/api/alembic/versions
-
-index: apps/api/alembic/versions/.pi-map.index.md
-
-## role
-Manages database schema evolution and version control for the API application using Alembic migration scripts.
-## files
-- 0001_initial_schema.py | Creates the initial database schema with five tables (users, ssh_keys, projects, git_repositories, user_configs) using Alembic migrations | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.String, call:postgresql.UUID, call:sa.DateTime, call:sa.func.now, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, call:op.create_index, call:op.f, call:sa.Text, call:sa.ForeignKeyConstraint, call:sa.Boolean, call:postgresql.JSONB, func:downgrade() → None, call:op.drop_table, call:op.drop_index, call:op.f | dep: alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
-- 0002_refresh_tokens.py | Alembic database migration that creates a refresh_tokens table with indexes for user authentication/session management | exp: func:upgrade() → None, call:op.get_bind, call:sa.inspect, call:inspector.has_table, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.String, call:sa.DateTime, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, call:inspector.get_indexes, call:op.f, call:op.create_index, func:downgrade() → None, call:op.get_bind, call:sa.inspect, call:inspector.has_table, call:inspector.get_indexes, call:op.f, call:op.drop_index, call:op.drop_table | dep: alembic, sqlalchemy.dialects, sqlalchemy, postgresql dialect
-- 0003_user_configs.py | Alembic database migration that creates a user_configs table with JSON configuration storage linked to users via foreign key | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.UUID, call:sa.JSON, call:sa.DateTime, call:sa.text, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, func:downgrade() → None, call:op.drop_table | dep: typing, alembic, sqlalchemy
-- 0004_tool_types.py | Alembic database migration that creates a tool_types table with metadata, templates, and user relationship columns | 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 UUID primary key, foreign key relationships, timestamps, and indexes for tracking deployed tool instances | 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, postgresql dialect
-- 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 for storing user tool configuration key-value pairs with optional project scoping | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.text, call:sa.String, call:sa.Text, call:sa.DateTime, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: typing, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
-- 0010_tool_type_default_port.py | Alembic database migration that adds a nullable default_port column to the tool_types table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.Integer, func:downgrade() → None, call:op.drop_column | dep: typing, alembic, sqlalchemy
-- 0011_tool_instance_tunnel_fields.py | Alembic database migration that adds public_url and tunnel_id columns to the tool_instances table for tunnel functionality. | 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 backfills default_port values for existing tool types and makes the column non-nullable | exp: func:upgrade() → None, call:op.execute, call:op.alter_column, call:sa.Integer, func:downgrade() → None, call:op.alter_column, call:sa.Integer | dep: typing, alembic, sqlalchemy
-- 0013_add_config_profiles.py | Database migration that adds config profiles, profile includes, profile mounts, and tool instance profile selection tables 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, start_command, working_directory, port, is_default) to config_profiles table, renames mount_path to target_path and adds mode/files columns to config_mounts table while removing source_profile_id and content columns | 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 combines 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 plural JSON interfaces column with singular interface_type and requires_port columns on tool_types table | exp: func:_get_dialect() → str, call:op.get_bind, func:upgrade() → None, call:_get_dialect, call:op.add_column, call:sa.Column, call:sa.String, call:sa.Boolean, call:op.execute, call:op.alter_column, call:op.drop_column, call:op.create_check_constraint, call:sa.text, func:downgrade() → None, call:_get_dialect, call:op.drop_constraint, call:op.add_column, call:sa.Column, call:postgresql.JSONB, call:sa.Text, call:op.execute, call:sa.JSON, call:op.drop_column | dep: typing, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
-- 069d3da4dc9b_add_ssh_key_id_to_config_profiles.py | Alembic database migration that adds an ssh_key_id foreign key column to the config_profiles table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.Uuid, call:sa.ForeignKey, func:downgrade() → None, call:op.drop_column | dep: alembic, sqlalchemy
-- 20260527160017_add_pi_agent_tool_type.py | Alembic database migration that adds a new "pi-agent" tool type with terminal-based Docker development environment configuration | 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 and clone_mode/branch columns to tool_instances | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:postgresql.UUID, call:op.create_foreign_key, call:sa.String, func:downgrade() → None, call:op.drop_column, call:op.drop_constraint | dep: alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
-- 2026_05_23_remove_is_builtin.py | Alembic database migration that removes the `is_builtin` column from the `tool_types` table with downgrade support to restore it. | exp: func:upgrade() → None, call:op.execute, func:downgrade() → None, call:op.add_column, call:sa.Column, call:sa.Boolean | dep: alembic, sqlalchemy
-- 2026_05_24_220141_add_startup_command.py | Alembic database migration that adds a nullable `startup_command` 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 selected_config_profile_id foreign key to tool_instances | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.text, call:sa.ForeignKey, call:sa.String, call:sa.Text, call:postgresql.JSONB, call:sa.Boolean, call:sa.DateTime, call:sa.PrimaryKeyConstraint, call:sa.UniqueConstraint, call:op.create_index, call:sa.Integer, call:op.add_column, func:downgrade() → None, call:op.drop_index, call:op.drop_column, call:op.drop_table | dep: typing, alembic, sqlalchemy.dialects, sqlalchemy, sqlalchemy.dialects.postgresql
-- 2026_05_26_add_git_mounts.py | 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 to support external repositories and expands alembic_version version_num column to prevent truncation. | 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 check status. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.Uuid, call:sa.String, call:sa.Text, call:sa.JSON, call:sa.DateTime, call:sa.func.now, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, call:sa.Boolean, call:sa.Integer, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy
-- 2026_05_28_add_terminal_sessions_table.py | Alembic database migration that creates a terminal_sessions table with foreign key to tool_instances for tracking terminal session lifecycle | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.UUID, call:sa.String, call:sa.DateTime, call:sa.text, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, call:op.f, func:downgrade() → None, call:op.drop_index, call:op.f, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy
-- 2026_05_28_add_tool_definition_manifests.py | Alembic database migration that creates a tool_definition_manifests table, adds manifest support to tool_types and tool_instances, and migrates the pi-agent tool from Dockerfile/compose templates to a JSON-based manifest system with a base Ubuntu image definition. | 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 | Database migration that drops the `tool_configs` and `config_folders` tables with conditional existence checks, and provides downgrade to recreate them. | exp: func:upgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:op.drop_table, func:downgrade() → None, call:op.create_table, call:sa.Column, call:sa.UUID, call:sa.String, call:sa.Text, call:sa.JSON, call:sa.Boolean, call:sa.TIMESTAMP, call:sa.func.now, call:sa.PrimaryKeyConstraint, call:sa.Integer | dep: typing, alembic, sqlalchemy
-- 2026_05_29_add_notifications_table.py | Alembic database migration that creates a notifications table with user-linked, categorized, and severity-based notification records including read/dismissed tracking and optimized indexes. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.Uuid, call:sa.String, call:sa.Text, call:sa.JSON, call:sa.DateTime, call:sa.func.now, call:sa.ForeignKeyConstraint, call:sa.PrimaryKeyConstraint, call:op.create_index, call:sa.text, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy
-- 2026_05_29_add_ssh_key_ids_to_tool_instances.py | Alembic database migration that adds a JSON ssh_key_ids column to the tool_instances table | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.JSON, func:downgrade() → None, call:op.drop_column | dep: alembic, sqlalchemy
-- 2026_05_29_drop_ssh_key_id_from_config_profiles.py | Alembic database migration that removes the ssh_key_id column from the config_profiles table | exp: func:upgrade() → None, call:op.drop_column, func:downgrade() → None, call:op.add_column, call:sa.Column, call:sa.Uuid, call:sa.ForeignKey | dep: alembic, sqlalchemy
-- 2026_05_29_fix_code_server_bind_addr.py | Alembic database migration that fixes code-server tool type compose templates by replacing deprecated --bind-addr flag with --host flag | exp: func:upgrade() → None, call:op.get_bind, call:conn.execute( sa.text(""" SELECT id, compose_template FROM tool_types WHERE name = 'code-server' AND compose_template LIKE '%--bind-addr%' """) ).fetchall, call:sa.text, call:compose_template.replace( "--bind-addr 0.0.0.0:8443", "--host 0.0.0.0" ).replace, call:print, func:downgrade() → None | dep: typing, alembic, sqlalchemy
-- 2026_05_29_fix_code_server_bind_addr_port.py | Alembic database migration that fixes code-server Docker compose templates by replacing broken `--host` flags with correct `--bind-addr 0.0.0.0:{port}` configurations in both database tool_type templates and on-disk instance compose files. | exp: func:_fix_tool_type_templates(conn) → None, call:conn.execute( sa.text(""" SELECT id, compose_template, default_port FROM tool_types WHERE name = 'code-server' AND compose_template LIKE '%--host%' """) ).fetchall, call:sa.text, call:compose_template.split, call:len, call:line.lstrip, call:new_lines.append, call:"\n".join, call:print, func:_fix_instance_compose_files(conn) → None, call:conn.execute( sa.text(""" SELECT column_name FROM information_schema.columns WHERE table_name = 'tool_instances' AND column_name = 'compose_path' """) ).fetchone, call:sa.text, call:print, call:conn.execute( sa.text(""" SELECT id, compose_path, tool_type_id FROM tool_instances WHERE compose_path IS NOT NULL """) ).fetchall, call:Path, call:path.exists, call:path.read_text, call:conn.execute( sa.text(""" SELECT default_port FROM tool_types WHERE id = :id """), {"id": tool_type_id}, ).fetchone, call:yaml.safe_load, call:data["services"].values, call:path.write_text, call:yaml.dump, func:upgrade() → None, call:op.get_bind, call:_fix_tool_type_templates, call:_fix_instance_compose_files, func:downgrade() → None | dep: typing, alembic, yaml, pathlib, sqlalchemy
-- 2026_05_29_fix_web_tool_bind_address.py | Alembic database migration that fixes code-server and jupyter-notebook tool 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 records and on-disk compose files. | exp: func:upgrade() → None, call:op.get_bind, call:conn.execute( sa.text(""" SELECT id, compose_template FROM tool_types WHERE name = 'code-server' """) ).fetchall, call:sa.text, call:yaml.safe_load, call:data["services"].values, call:svc.get, call:yaml.dump, call:print, call:conn.execute( sa.text(""" SELECT column_name FROM information_schema.columns WHERE table_name = 'tool_instances' AND column_name = 'compose_path' """) ).fetchone, call:conn.execute( sa.text(""" SELECT id, compose_path FROM tool_instances WHERE compose_path IS NOT NULL """) ).fetchall, call:Path, call:path.exists, call:path.read_text, call:path.write_text, func:downgrade() → None | dep: collections.abc, alembic, yaml, pathlib, sqlalchemy
-- 2026_05_29_remove_ssh_keys_mount_from_manifest.py | Alembic database migration that removes (and can restore) the ssh_keys mount from the pi-agent tool definition manifest stored as JSON | 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 indexes and adds a workspace_id foreign key to tool_instances | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:sa.Uuid, call:sa.String, call:sa.ForeignKey, call:sa.DateTime, call:sa.text, call:sa.UniqueConstraint, call:op.create_index, call:op.add_column, func:downgrade() → None, call:op.drop_index, call:op.drop_column, call:op.drop_table | dep: collections.abc, alembic, sqlalchemy
-- 2026_06_13_make_clone_mode_nullable.py | Alembic database migration to make the `clone_mode` column nullable in the `tool_instances` table | exp: func:upgrade() → None, call:op.alter_column, call:sa.String, func:downgrade() → None, call:op.alter_column, call:sa.String | dep: alembic, sqlalchemy
-- 2026_06_14_104415_add_tool_type_home_directory.py | Alembic database migration that adds a home_directory column to tool_types table and updates template strings from /workspace to a configurable path | exp: func:upgrade() → None, call:op.add_column, call:sa.Column, call:sa.String, call:op.execute, call:sa.update(tool_types) .where(tool_types.c.compose_template.is_not(None)) .values, call:tool_types.c.compose_template.is_not, call:sa.func.replace, call:sa.update(tool_types) .where(tool_types.c.dockerfile_template.is_not(None)) .values, call:tool_types.c.dockerfile_template.is_not, func:downgrade() → None, call:op.execute, call:sa.update(tool_types) .where(tool_types.c.compose_template.is_not(None)) .values, call:tool_types.c.compose_template.is_not, call:sa.func.replace, call:sa.update(tool_types) .where(tool_types.c.dockerfile_template.is_not(None)) .values, call:tool_types.c.dockerfile_template.is_not, call:op.drop_column | dep: typing, alembic, sqlalchemy.sql, sqlalchemy
-- 2026_06_14_182955_fix_pi_agent_home_directory_mount.py | Alembic database migration that updates the pi-agent tool definition manifest to mount repos under the home directory instead of /workspace | exp: func:_find_pi_agent_manifest(conn: sa.Connection) → tuple[Union[str, None], Union[dict, None]], call:conn.execute( sa.select(tool_definition_manifests.c.id, tool_definition_manifests.c.manifest) .where(tool_definition_manifests.c.name == "pi-agent") ).fetchone, call:sa.select(tool_definition_manifests.c.id, tool_definition_manifests.c.manifest) .where, call:dict, func:_update_manifest(conn: sa.Connection, manifest_id: str, manifest: dict) → None, call:conn.execute, call:sa.update(tool_definition_manifests) .where(tool_definition_manifests.c.id == manifest_id) .values, func:upgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.get, call:mount.get, call:manifest.setdefault, call:_update_manifest, func:downgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.get, call:mount.get, call:manifest.setdefault, call:_update_manifest | dep: typing, alembic, sqlalchemy.sql, sqlalchemy
-- 2026_06_15_090500_remove_pi_agent_explicit_repo_mount.py | Alembic database migration that removes explicit repo mounts from pi-agent tool definition manifests since they are now synthesized by compile_compose | exp: func:_find_pi_agent_manifest(conn: sa.Connection) → tuple[Union[str, None], Union[dict, None]], call:conn.execute( sa.select( tool_definition_manifests.c.id, tool_definition_manifests.c.manifest ).where(tool_definition_manifests.c.name == "pi-agent") ).fetchone, call:sa.select( tool_definition_manifests.c.id, tool_definition_manifests.c.manifest ).where, call:dict, func:_update_manifest(conn: sa.Connection, manifest_id: str, manifest: dict) → None, call:conn.execute, call:sa.update(tool_definition_manifests) .where(tool_definition_manifests.c.id == manifest_id) .values, func:upgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.get, call:mount.get, call:_update_manifest, func:downgrade() → None, call:op.get_bind, call:_find_pi_agent_manifest, call:manifest.setdefault, call:any, call:mount.get, call:mounts.append, call:_update_manifest | dep: typing, alembic, sqlalchemy.sql, sqlalchemy
-- 398082499c30_add_tool_config_fields.py | Alembic database migration that adds configuration fields (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 branches (removing is_builtin and adding config_profiles) with no actual schema changes | exp: func:upgrade() → None, func:downgrade() → None | dep: alembic
-- 86cec91fdb00_merge_profile_resolver_and_workspaces_.py | Alembic database migration that merges two divergent migration branches (profile resolver and workspaces) into a single head | exp: func:upgrade() → None, func:downgrade() → None | dep: alembic
-- 8c6d1dbd4798_remove_pi_config_and_state_mounts_from_.py | Alembic database migration that removes pi_state and pi_config mounts from the pi-agent manifest in upgrade, and restores them in downgrade | exp: func:_load_manifest(manifest_json), call:isinstance, call:json.loads, func:upgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:_load_manifest, call:manifest.get, call:len, call:m.get, call:json.dumps, func:downgrade() → None, call:op.get_bind, call:conn.execute, call:sa.text, call:result.fetchone, call:_load_manifest, call:manifest.get, call:m.get, call:mounts.append, call:json.dumps | dep: json, alembic, sqlalchemy
-- 8ed7dd80973d_create_config_folders_table.py | Creates a database migration that adds a config_folders table for storing user configuration folders with JSONB metadata, foreign key relationships, and indexing. | exp: func:upgrade() → None, call:op.create_table, call:sa.Column, call:postgresql.UUID, call:sa.text, call:sa.ForeignKey, call:sa.String, call:sa.Text, call:postgresql.JSONB, call:sa.Boolean, call:sa.DateTime, call:sa.UniqueConstraint, call:op.create_index, func:downgrade() → None, call:op.drop_index, call:op.drop_table | dep: alembic, sqlalchemy.dialects, sqlalchemy, postgresql dialect
-- af8512103d67_add_tool_type_fields.py | Alembic database migration that adds 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 parent revisions (single_interface and clone_mode) into a single branch point with no actual schema changes | exp: func:upgrade() → None, func:downgrade() → None | dep: typing, alembic
-- fc8f1a20cbf6_merge_home_directory_and_pi_agent_mount_.py | Alembic database migration that merges two branch heads (home directory and pi agent mount cleanup) into a single revision point | exp: func:upgrade() → None, func:downgrade() → None | dep: alembic
-## arch
-Linear migration history with branching/merge resolution pattern; each migration is an immutable, timestamped or sequenced script containing declarative SQLAlchemy operations (create_table, add_column, drop_column) with bidirectional upgrade/downgrade functions; includes data migrations, idempotent guards, and cross-references to on-disk file mutations.
-## tags
-column, table, call:op.drop, downgrade, upgrade, alembic, key, call:sa.text
-## symbols
-- upgrade
-- downgrade
-- _table_exists
-- _column_exists
-- _index_exists
-- _foreign_key_exists
-- _foreign_key_names_for_column
-- _get_dialect
-## workflows
-- change versions behavior
-  read: 0001_initial_schema.py, 0002_refresh_tokens.py, 0003_user_configs.py
-- change versions CLI
-  read: 2026_05_24_220141_add_startup_command.py, 2026_05_29_remove_lsio_command_override.py
-- change versions config
-  read: 0003_user_configs.py, 0009_tool_configs.py, 0013_add_config_profiles.py
-## dirty
--

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

@@ -5,7 +5,7 @@ Revises: 0012_default_port_req
 Create Date: 2026-05-24 12:00:00.000000
 
 """
-from collections.abc import Sequence
+from typing import Sequence, Union
 
 from alembic import op
 import sqlalchemy as sa
@@ -13,181 +13,81 @@ from sqlalchemy.dialects import postgresql
 
 # revision identifiers, used by Alembic.
 revision: str = "0013_add_config_profiles"
-down_revision: str | None = "0012_default_port_req"
-branch_labels: str | Sequence[str] | None = None
-depends_on: str | Sequence[str] | None = None
-
-
-def _table_exists(table_name: str) -> bool:
-    return sa.inspect(op.get_bind()).has_table(table_name)
-
-
-def _column_exists(table_name: str, column_name: str) -> bool:
-    if not _table_exists(table_name):
-        return False
-    return column_name in {
-        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
-    }
-
-
-def _index_exists(table_name: str, index_name: str) -> bool:
-    if not _table_exists(table_name):
-        return False
-    return index_name in {
-        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
-    }
-
-
-def _foreign_key_exists(
-    table_name: str,
-    constrained_columns: list[str],
-    referred_table: str,
-) -> bool:
-    if not _table_exists(table_name):
-        return False
-    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
-        if (
-            foreign_key.get("constrained_columns") == constrained_columns
-            and foreign_key.get("referred_table") == referred_table
-        ):
-            return True
-    return False
+down_revision: Union[str, None] = "0012_default_port_req"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
 
 
 def upgrade() -> None:
-    # Earlier branches may already have created config_profiles. Keep this
-    # migration defensive so databases can converge onto the current graph.
-    if not _table_exists("config_profiles"):
-        op.create_table(
-            "config_profiles",
-            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
-            sa.Column("user_id", postgresql.UUID(as_uuid=True), nullable=False),
-            sa.Column("name", sa.String(length=255), nullable=False),
-            sa.Column("description", sa.Text(), nullable=True),
-            sa.Column(
-                "created_at",
-                sa.DateTime(timezone=True),
-                server_default=sa.text("NOW()"),
-                nullable=False,
-            ),
-            sa.Column(
-                "updated_at",
-                sa.DateTime(timezone=True),
-                server_default=sa.text("NOW()"),
-                nullable=False,
-            ),
-            sa.ForeignKeyConstraint(["user_id"], ["users.id"], ondelete="CASCADE"),
-            sa.PrimaryKeyConstraint("id"),
-            sa.UniqueConstraint(
-                "user_id", "name", name="uq_config_profiles_user_name"
-            ),
-        )
-    if not _index_exists("config_profiles", "idx_config_profiles_user"):
-        op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
+    # Create config_profiles table
+    op.create_table(
+        "config_profiles",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("user_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("name", sa.String(length=255), nullable=False),
+        sa.Column("description", sa.Text(), nullable=True),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.ForeignKeyConstraint(["user_id"], ["users.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
+    )
+    op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
 
-    if not _table_exists("config_includes"):
-        op.create_table(
-            "config_includes",
-            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
-            sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
-            sa.Column(
-                "included_profile_id", postgresql.UUID(as_uuid=True), nullable=False
-            ),
-            sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
-            sa.Column(
-                "created_at",
-                sa.DateTime(timezone=True),
-                server_default=sa.text("NOW()"),
-                nullable=False,
-            ),
-            sa.Column(
-                "updated_at",
-                sa.DateTime(timezone=True),
-                server_default=sa.text("NOW()"),
-                nullable=False,
-            ),
-            sa.ForeignKeyConstraint(
-                ["profile_id"], ["config_profiles.id"], ondelete="CASCADE"
-            ),
-            sa.ForeignKeyConstraint(
-                ["included_profile_id"],
-                ["config_profiles.id"],
-                ondelete="CASCADE",
-            ),
-            sa.PrimaryKeyConstraint("id"),
-            sa.UniqueConstraint(
-                "profile_id", "included_profile_id", name="uq_config_includes_pair"
-            ),
-        )
-    if not _index_exists("config_includes", "idx_config_includes_profile"):
-        op.create_index("idx_config_includes_profile", "config_includes", ["profile_id"])
-    if not _index_exists("config_includes", "idx_config_includes_included"):
-        op.create_index(
-            "idx_config_includes_included", "config_includes", ["included_profile_id"]
-        )
+    # Create config_includes table
+    op.create_table(
+        "config_includes",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("included_profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.ForeignKeyConstraint(["profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["included_profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("profile_id", "included_profile_id", name="uq_config_includes_pair"),
+    )
+    op.create_index("idx_config_includes_profile", "config_includes", ["profile_id"])
+    op.create_index("idx_config_includes_included", "config_includes", ["included_profile_id"])
 
-    if not _table_exists("config_mounts"):
-        op.create_table(
-            "config_mounts",
-            sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
-            sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
-            sa.Column("mount_path", sa.String(length=1024), nullable=False),
-            sa.Column("content", sa.Text(), nullable=True),
-            sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
-            sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
-            sa.Column(
-                "created_at",
-                sa.DateTime(timezone=True),
-                server_default=sa.text("NOW()"),
-                nullable=False,
-            ),
-            sa.Column(
-                "updated_at",
-                sa.DateTime(timezone=True),
-                server_default=sa.text("NOW()"),
-                nullable=False,
-            ),
-            sa.ForeignKeyConstraint(
-                ["profile_id"], ["config_profiles.id"], ondelete="CASCADE"
-            ),
-            sa.ForeignKeyConstraint(
-                ["source_profile_id"], ["config_profiles.id"], ondelete="SET NULL"
-            ),
-            sa.PrimaryKeyConstraint("id"),
-        )
-    if not _index_exists("config_mounts", "idx_config_mounts_profile"):
-        op.create_index("idx_config_mounts_profile", "config_mounts", ["profile_id"])
+    # Create config_mounts table
+    op.create_table(
+        "config_mounts",
+        sa.Column("id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("profile_id", postgresql.UUID(as_uuid=True), nullable=False),
+        sa.Column("mount_path", sa.String(length=1024), nullable=False),
+        sa.Column("content", sa.Text(), nullable=True),
+        sa.Column("source_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+        sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
+        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
+        sa.ForeignKeyConstraint(["profile_id"], ["config_profiles.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["source_profile_id"], ["config_profiles.id"], ondelete="SET NULL"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("idx_config_mounts_profile", "config_mounts", ["profile_id"])
 
-    if not _column_exists("tool_instances", "selected_profile_id"):
-        op.add_column(
-            "tool_instances",
-            sa.Column("selected_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
-        )
-    if not _foreign_key_exists(
-        "tool_instances", ["selected_profile_id"], "config_profiles"
-    ):
-        op.create_foreign_key(
-            "fk_tool_instances_selected_profile",
-            "tool_instances",
-            "config_profiles",
-            ["selected_profile_id"],
-            ["id"],
-            ondelete="SET NULL",
-        )
-    if not _index_exists("tool_instances", "idx_tool_instances_selected_profile"):
-        op.create_index(
-            "idx_tool_instances_selected_profile",
-            "tool_instances",
-            ["selected_profile_id"],
-        )
+    # Add selected_profile_id to tool_instances
+    op.add_column(
+        "tool_instances",
+        sa.Column("selected_profile_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.create_foreign_key(
+        "fk_tool_instances_selected_profile",
+        "tool_instances",
+        "config_profiles",
+        ["selected_profile_id"],
+        ["id"],
+        ondelete="SET NULL",
+    )
+    op.create_index("idx_tool_instances_selected_profile", "tool_instances", ["selected_profile_id"])
 
 
 def downgrade() -> None:
     # Remove selected_profile_id from tool_instances
     op.drop_index("idx_tool_instances_selected_profile", table_name="tool_instances")
-    op.drop_constraint(
-        "fk_tool_instances_selected_profile", "tool_instances", type_="foreignkey"
-    )
+    op.drop_constraint("fk_tool_instances_selected_profile", "tool_instances", type_="foreignkey")
     op.drop_column("tool_instances", "selected_profile_id")
 
     # Drop config_mounts

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

@@ -1,29 +0,0 @@
-"""add probe_result to tool_instances
-
-Revision ID: 0013_add_probe_result
-Revises: 0012_default_port_req
-Create Date: 2026-05-22 21:45:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import postgresql
-
-# revision identifiers, used by Alembic.
-revision: str = "0013_add_probe_result"
-down_revision: Union[str, None] = "0012_default_port_req"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    op.add_column(
-        "tool_instances",
-        sa.Column("probe_result", postgresql.JSON, nullable=True)
-    )
-
-
-def downgrade() -> None:
-    op.drop_column("tool_instances", "probe_result")

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

@@ -5,7 +5,7 @@ Revises: 0013_add_config_profiles
 Create Date: 2026-05-24 14:00:00.000000
 
 """
-from collections.abc import Sequence
+from typing import Sequence, Union
 
 from alembic import op
 import sqlalchemy as sa
@@ -13,141 +13,82 @@ from sqlalchemy.dialects import postgresql
 
 # revision identifiers, used by Alembic.
 revision: str = "0014_add_profile_resolver_fields"
-down_revision: str | None = "0013_add_config_profiles"
-branch_labels: str | Sequence[str] | None = None
-depends_on: str | Sequence[str] | None = None
-
-
-def _table_exists(table_name: str) -> bool:
-    return sa.inspect(op.get_bind()).has_table(table_name)
-
-
-def _column_exists(table_name: str, column_name: str) -> bool:
-    if not _table_exists(table_name):
-        return False
-    return column_name in {
-        column["name"] for column in sa.inspect(op.get_bind()).get_columns(table_name)
-    }
-
-
-def _index_exists(table_name: str, index_name: str) -> bool:
-    if not _table_exists(table_name):
-        return False
-    return index_name in {
-        index["name"] for index in sa.inspect(op.get_bind()).get_indexes(table_name)
-    }
-
-
-def _foreign_key_exists(
-    table_name: str,
-    constrained_columns: list[str],
-    referred_table: str,
-) -> bool:
-    if not _table_exists(table_name):
-        return False
-    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
-        if (
-            foreign_key.get("constrained_columns") == constrained_columns
-            and foreign_key.get("referred_table") == referred_table
-        ):
-            return True
-    return False
-
-
-def _foreign_key_names_for_column(table_name: str, column_name: str) -> list[str]:
-    if not _table_exists(table_name):
-        return []
-    names: list[str] = []
-    for foreign_key in sa.inspect(op.get_bind()).get_foreign_keys(table_name):
-        if column_name in foreign_key.get("constrained_columns", []):
-            name = foreign_key.get("name")
-            if name:
-                names.append(name)
-    return names
+down_revision: Union[str, None] = "0013_add_config_profiles"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
 
 
 def upgrade() -> None:
-    if not _column_exists("config_profiles", "project_id"):
-        op.add_column(
-            "config_profiles",
-            sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
-        )
-    if not _column_exists("config_profiles", "tool_type_id"):
-        op.add_column(
-            "config_profiles",
-            sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=True),
-        )
-    if not _column_exists("config_profiles", "environment_variables"):
-        op.add_column(
-            "config_profiles",
-            sa.Column("environment_variables", sa.JSON(), nullable=True),
-        )
-    if not _column_exists("config_profiles", "start_command"):
-        op.add_column(
-            "config_profiles",
-            sa.Column("start_command", sa.Text(), nullable=True),
-        )
-    if not _column_exists("config_profiles", "working_directory"):
-        op.add_column(
-            "config_profiles",
-            sa.Column("working_directory", sa.Text(), nullable=True),
-        )
-    if not _column_exists("config_profiles", "port"):
-        op.add_column("config_profiles", sa.Column("port", sa.Integer(), nullable=True))
-    if not _column_exists("config_profiles", "is_default"):
-        op.add_column(
-            "config_profiles",
-            sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
-        )
-
-    if not _foreign_key_exists("config_profiles", ["project_id"], "projects"):
-        op.create_foreign_key(
-            "fk_config_profiles_project",
-            "config_profiles",
-            "projects",
-            ["project_id"],
-            ["id"],
-            ondelete="CASCADE",
-        )
-    if not _foreign_key_exists("config_profiles", ["tool_type_id"], "tool_types"):
-        op.create_foreign_key(
-            "fk_config_profiles_tool_type",
-            "config_profiles",
-            "tool_types",
-            ["tool_type_id"],
-            ["id"],
-            ondelete="CASCADE",
-        )
-
-    if not _index_exists("config_profiles", "idx_config_profiles_project"):
-        op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
-    if not _index_exists("config_profiles", "idx_config_profiles_tool_type"):
-        op.create_index(
-            "idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"]
-        )
-
-    if _column_exists("config_mounts", "mount_path") and not _column_exists(
-        "config_mounts", "target_path"
-    ):
-        op.alter_column("config_mounts", "mount_path", new_column_name="target_path")
-    if not _column_exists("config_mounts", "mode"):
-        op.add_column(
-            "config_mounts",
-            sa.Column("mode", sa.String(length=10), nullable=False, server_default="rw"),
-        )
-    if not _column_exists("config_mounts", "files"):
-        op.add_column(
-            "config_mounts",
-            sa.Column("files", sa.JSON(), nullable=True),
-        )
-    for constraint_name in _foreign_key_names_for_column(
-        "config_mounts", "source_profile_id"
-    ):
-        op.drop_constraint(constraint_name, "config_mounts", type_="foreignkey")
-    if _column_exists("config_mounts", "content"):
-        op.drop_column("config_mounts", "content")
-    if _column_exists("config_mounts", "source_profile_id"):
-        op.drop_column("config_mounts", "source_profile_id")
+    # Add fields to config_profiles
+    op.add_column(
+        "config_profiles",
+        sa.Column("project_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("environment_variables", sa.JSON(), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("start_command", sa.Text(), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("working_directory", sa.Text(), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("port", sa.Integer(), nullable=True),
+    )
+    op.add_column(
+        "config_profiles",
+        sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
+    )
+    
+    # Add foreign keys for project and tool_type
+    op.create_foreign_key(
+        "fk_config_profiles_project",
+        "config_profiles",
+        "projects",
+        ["project_id"],
+        ["id"],
+        ondelete="CASCADE",
+    )
+    op.create_foreign_key(
+        "fk_config_profiles_tool_type",
+        "config_profiles",
+        "tool_types",
+        ["tool_type_id"],
+        ["id"],
+        ondelete="CASCADE",
+    )
+    
+    # Create indices
+    op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
+    op.create_index("idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"])
+    
+    # Alter config_mounts: rename mount_path to target_path, add mode, change content to files JSON
+    op.alter_column("config_mounts", "mount_path", new_column_name="target_path")
+    op.add_column(
+        "config_mounts",
+        sa.Column("mode", sa.String(length=10), nullable=False, server_default="rw"),
+    )
+    op.add_column(
+        "config_mounts",
+        sa.Column("files", sa.JSON(), nullable=True),
+    )
+    # Drop the source_profile foreign key if it exists
+    op.drop_constraint(
+        "config_mounts_source_profile_id_fkey",
+        "config_mounts",
+        type_="foreignkey",
+    )
+    op.drop_column("config_mounts", "content")
+    op.drop_column("config_mounts", "source_profile_id")
 
 
 def downgrade() -> None:
@@ -163,13 +104,11 @@ def downgrade() -> None:
     op.drop_column("config_mounts", "files")
     op.drop_column("config_mounts", "mode")
     op.alter_column("config_mounts", "target_path", new_column_name="mount_path")
-
+    
     # Restore config_profiles
     op.drop_index("idx_config_profiles_tool_type", table_name="config_profiles")
     op.drop_index("idx_config_profiles_project", table_name="config_profiles")
-    op.drop_constraint(
-        "fk_config_profiles_tool_type", "config_profiles", type_="foreignkey"
-    )
+    op.drop_constraint("fk_config_profiles_tool_type", "config_profiles", type_="foreignkey")
     op.drop_constraint("fk_config_profiles_project", "config_profiles", type_="foreignkey")
     op.drop_column("config_profiles", "is_default")
     op.drop_column("config_profiles", "port")

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

@@ -1,23 +0,0 @@
-"""merge migration heads
-
-Revision ID: 0014_merge_heads
-Revises: 0013_add_probe_result, 8ed7dd80973d
-Create Date: 2026-05-22 21:50:00.000000
-
-"""
-from typing import Sequence, Union
-
-
-# revision identifiers, used by Alembic.
-revision: str = "0014_merge_heads"
-down_revision: Union[str, Sequence[str], None] = ("0013_add_probe_result", "8ed7dd80973d")
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    pass
-
-
-def downgrade() -> None:
-    pass

apps/api/alembic/versions/0015_single_interface.py

@@ -1,109 +0,0 @@
-"""replace interfaces with interface_type and add requires_port
-
-Revision ID: 0015_single_interface
-Revises: 0014_merge_heads
-Create Date: 2026-05-22 22:00:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import postgresql
-
-# revision identifiers, used by Alembic.
-revision: str = "0015_single_interface"
-down_revision: Union[str, Sequence[str], None] = "0014_merge_heads"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def _get_dialect() -> str:
-    """Get the current database dialect name."""
-    conn = op.get_bind()
-    return conn.dialect.name
-
-
-def upgrade() -> None:
-    dialect = _get_dialect()
-    
-    # Add new columns
-    op.add_column('tool_types', sa.Column('interface_type', sa.String(20), nullable=True))
-    op.add_column('tool_types', sa.Column('requires_port', sa.Boolean(), nullable=False, server_default='true'))
-    
-    # Migrate data: take first element from interfaces JSON array
-    if dialect == 'postgresql':
-        op.execute("""
-            UPDATE tool_types 
-            SET interface_type = COALESCE(
-                (SELECT elem FROM jsonb_array_elements_text(interfaces::jsonb) AS elem LIMIT 1),
-                'web'
-            ),
-            requires_port = CASE 
-                WHEN COALESCE(
-                    (SELECT elem FROM jsonb_array_elements_text(interfaces::jsonb) AS elem LIMIT 1),
-                    'web'
-                ) = 'web' THEN true
-                ELSE false
-            END
-        """)
-    else:
-        # SQLite: interfaces is stored as JSON text, extract first array element
-        op.execute("""
-            UPDATE tool_types 
-            SET interface_type = COALESCE(
-                (SELECT json_extract(value, '$[0]') 
-                 FROM json_each(interfaces) AS value 
-                 WHERE json_valid(interfaces) 
-                 LIMIT 1),
-                'web'
-            ),
-            requires_port = CASE 
-                WHEN COALESCE(
-                    (SELECT json_extract(value, '$[0]') 
-                     FROM json_each(interfaces) AS value 
-                     WHERE json_valid(interfaces) 
-                     LIMIT 1),
-                    'web'
-                ) = 'web' THEN true
-                ELSE false
-            END
-        """)
-    
-    # Make interface_type non-nullable after data migration
-    op.alter_column('tool_types', 'interface_type', nullable=False)
-    
-    # Drop old interfaces column
-    op.drop_column('tool_types', 'interfaces')
-    
-    # Add CHECK constraint for interface_type (only on PostgreSQL; SQLite supports it too)
-    op.create_check_constraint('chk_interface_type', 'tool_types', sa.text("interface_type IN ('web', 'terminal')"))
-
-
-def downgrade() -> None:
-    dialect = _get_dialect()
-    
-    # Drop CHECK constraint
-    op.drop_constraint('chk_interface_type', 'tool_types', type_='check')
-    
-    # Add back interfaces column
-    if dialect == 'postgresql':
-        op.add_column('tool_types', sa.Column('interfaces', postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default='["web"]'))
-        
-        # Migrate data back: wrap interface_type in array
-        op.execute("""
-            UPDATE tool_types 
-            SET interfaces = jsonb_build_array(interface_type)
-        """)
-    else:
-        op.add_column('tool_types', sa.Column('interfaces', sa.JSON(), nullable=False, server_default='["web"]'))
-        
-        # Migrate data back: wrap interface_type in array for SQLite
-        op.execute("""
-            UPDATE tool_types 
-            SET interfaces = json_array(interface_type)
-        """)
-    
-    # Drop new columns
-    op.drop_column('tool_types', 'requires_port')
-    op.drop_column('tool_types', 'interface_type')

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

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

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

@@ -1,129 +0,0 @@
-"""add pi agent tool type
-
-Revision ID: 20260527_160017_add_pi_agent
-Revises: f3d2dc90ba3a
-Create Date: 2026-05-27T16:00:17
-
-"""
-
-import json
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-import uuid
-
-# revision identifiers, used by Alembic.
-revision: str = "20260527_160017_add_pi_agent"
-down_revision: Union[str, None] = "2026_05_27_external_repos"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-PI_AGENT_ID = uuid.UUID("d07b8376-2151-4119-8c1d-27f792aae9a3")
-
-
-def upgrade() -> None:
-    # Check if pi-agent already exists
-    conn = op.get_bind()
-    result = conn.execute(
-        sa.text("SELECT id FROM tool_types WHERE name = 'pi-agent'")
-    ).fetchone()
-    
-    if result is None:
-        conn.execute(
-            sa.text("""
-                INSERT INTO tool_types (
-                    id, name, display_name, description, category,
-                    interface_type, requires_port, default_port,
-                    definition_type, compose_template, dockerfile_template, required_variables,
-                    created_at, updated_at
-                ) VALUES (
-                    :id, :name, :display_name, :description, :category,
-                    :interface_type, :requires_port, :default_port,
-                    :definition_type, :compose_template, :dockerfile_template, :required_variables,
-                    now(), now()
-                )
-            """),
-            {
-                "id": PI_AGENT_ID,
-                "name": "pi-agent",
-                "display_name": "Pi Agent",
-                "description": "Pi coding agent terminal environment with nvim, ranger, and tmux",
-                "category": "development",
-                "interface_type": "terminal",
-                "requires_port": False,
-                "default_port": 0,
-                "definition_type": "dockerfile",
-                "compose_template": """services:
-  app:
-    build: .
-    stdin_open: true
-    tty: true
-    volumes:
-      - ${REPO_PATH}:/workspace
-    working_dir: /workspace
-    command: /bin/bash""",
-                "dockerfile_template": """# Pi Coding Agent - Terminal-based coding harness
-FROM ubuntu:24.04
-
-ENV DEBIAN_FRONTEND=noninteractive
-
-# Install base dependencies
-RUN apt-get update && apt-get install -y \\
-    curl \\
-    wget \\
-    git \\
-    neovim \\
-    ranger \\
-    tmux \\
-    htop \\
-    tree \\
-    jq \\
-    ca-certificates \\
-    python3 \\
-    python3-pip \\
-    build-essential \\
-    && rm -rf /var/lib/apt/lists/*
-
-# Install Node.js (required for Pi)
-RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \\
-    && apt-get install -y nodejs \\
-    && rm -rf /var/lib/apt/lists/*
-
-# Install Pi Coding Agent globally
-RUN npm install -g --ignore-scripts @earendil-works/pi-coding-agent
-
-# Create non-root user
-RUN useradd -m -s /bin/bash user
-WORKDIR /home/user
-
-# Set up git
-RUN git config --global init.defaultBranch main \\
-    && git config --global user.email "dev@headquarter.local" \\
-    && git config --global user.name "Developer"
-
-# Create default tmux config
-RUN printf '%s\\n' 'set -g mouse on' 'set -g default-terminal "screen-256color"' > /home/user/.tmux.conf
-
-# Create default ranger config
-RUN mkdir -p /home/user/.config/ranger \\
-    && printf '%s\\n' 'set preview_files true' 'set use_preview_script true' > /home/user/.config/ranger/rc.conf
-
-# Set up Pi config directory
-RUN mkdir -p /home/user/.pi/agent
-
-USER user
-
-# Default to bash (Pi is invoked manually via `pi` command)
-CMD ["/bin/bash"]""",
-                "required_variables": json.dumps(["REPO_PATH"]),
-            }
-        )
-
-
-def downgrade() -> None:
-    conn = op.get_bind()
-    conn.execute(
-        sa.text("DELETE FROM tool_types WHERE name = 'pi-agent'")
-    )

apps/api/alembic/versions/2026_05_22_add_clone_mode.py

@@ -1,36 +0,0 @@
-"""add_clone_mode_and_ssh_key_id
-
-Revision ID: 2026_05_22_add_clone_mode
-Revises: 0014_merge_heads
-Create Date: 2026-05-22 20:30:00.000000
-"""
-
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import postgresql
-
-# revision identifiers, used by Alembic.
-revision = '2026_05_22_add_clone_mode'
-down_revision = '0015_single_interface'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # Add ssh_key_id to git_repositories
-    op.add_column('git_repositories', sa.Column('ssh_key_id', postgresql.UUID(), nullable=True))
-    op.create_foreign_key('fk_git_repositories_ssh_key', 'git_repositories', 'ssh_keys', ['ssh_key_id'], ['id'])
-    
-    # Add clone_mode and branch to tool_instances
-    op.add_column('tool_instances', sa.Column('clone_mode', sa.String(20), nullable=False, server_default='mount'))
-    op.add_column('tool_instances', sa.Column('branch', sa.String(255), nullable=True, server_default='main'))
-
-
-def downgrade() -> None:
-    # Drop columns from tool_instances
-    op.drop_column('tool_instances', 'branch')
-    op.drop_column('tool_instances', 'clone_mode')
-    
-    # Drop ssh_key_id from git_repositories
-    op.drop_constraint('fk_git_repositories_ssh_key', 'git_repositories', type_='foreignkey')
-    op.drop_column('git_repositories', 'ssh_key_id')

apps/api/alembic/versions/2026_05_23_remove_is_builtin.py

@@ -1,25 +0,0 @@
-"""remove_is_builtin_from_tool_types
-
-Revision ID: 2026_05_23_remove_is_builtin
-Revises: 2026_05_22_add_clone_mode
-Create Date: 2026-05-23 14:30:00.000000
-"""
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision = '2026_05_23_remove_is_builtin'
-down_revision = 'f3d2dc90ba3a'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # Drop the is_builtin column from tool_types
-    op.execute("ALTER TABLE tool_types DROP COLUMN IF EXISTS is_builtin")
-
-
-def downgrade() -> None:
-    # Add the is_builtin column back to tool_types
-    op.add_column('tool_types', sa.Column('is_builtin', sa.Boolean(), nullable=False, server_default='false'))

apps/api/alembic/versions/2026_05_24_220141_add_startup_command.py

@@ -1,30 +0,0 @@
-"""add startup_command to tool_types
-
-Revision ID: 2026_05_24_220141
-Revises: 6fc7bfcf199f
-Create Date: 2026-05-24 22:01:41.000000
-
-"""
-
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_24_220141"
-down_revision: Union[str, Sequence[str], None] = "6fc7bfcf199f"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    op.add_column(
-        "tool_types",
-        sa.Column("startup_command", sa.Text(), nullable=True),
-    )
-
-
-def downgrade() -> None:
-    op.drop_column("tool_types", "startup_command")

apps/api/alembic/versions/2026_05_24_add_config_profiles.py

@@ -1,86 +0,0 @@
-"""add_config_profiles
-
-Revision ID: 2026_05_24_add_config_profiles
-Revises: f3d2dc90ba3a
-Create Date: 2026-05-24 14:00:00.000000
-"""
-
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import postgresql
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_24_add_config_profiles"
-down_revision: Union[str, Sequence[str], None] = "f3d2dc90ba3a"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    # Create config_profiles table
-    op.create_table(
-        "config_profiles",
-        sa.Column("id", postgresql.UUID(as_uuid=True), server_default=sa.text("gen_random_uuid()"), nullable=False),
-        sa.Column("user_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("users.id", ondelete="CASCADE"), nullable=False),
-        sa.Column("name", sa.String(255), nullable=False),
-        sa.Column("description", sa.Text(), nullable=True),
-        sa.Column("project_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("projects.id", ondelete="CASCADE"), nullable=True),
-        sa.Column("tool_type_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("tool_types.id", ondelete="CASCADE"), nullable=True),
-        sa.Column("env_vars", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
-        sa.Column("runtime_hints", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
-        sa.Column("mounts", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="[]"),
-        sa.Column("files", postgresql.JSONB(astext_type=sa.Text()), nullable=False, server_default="{}"),
-        sa.Column("is_default", sa.Boolean(), nullable=False, server_default="false"),
-        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
-        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
-        sa.PrimaryKeyConstraint("id"),
-        sa.UniqueConstraint("user_id", "name", name="uq_config_profiles_user_name"),
-    )
-
-    # Create indexes for config_profiles
-    op.create_index("idx_config_profiles_user", "config_profiles", ["user_id"])
-    op.create_index("idx_config_profiles_project", "config_profiles", ["project_id"])
-    op.create_index("idx_config_profiles_tool_type", "config_profiles", ["tool_type_id"])
-
-    # Create config_profile_includes table
-    op.create_table(
-        "config_profile_includes",
-        sa.Column("id", postgresql.UUID(as_uuid=True), server_default=sa.text("gen_random_uuid()"), nullable=False),
-        sa.Column("profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False),
-        sa.Column("included_profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="CASCADE"), nullable=False),
-        sa.Column("order_index", sa.Integer(), nullable=False, server_default="0"),
-        sa.Column("created_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
-        sa.Column("updated_at", sa.DateTime(timezone=True), server_default=sa.text("NOW()"), nullable=False),
-        sa.PrimaryKeyConstraint("id"),
-        sa.UniqueConstraint("profile_id", "included_profile_id", name="uq_config_profile_includes"),
-    )
-
-    # Create indexes for config_profile_includes
-    op.create_index("idx_config_profile_includes_profile", "config_profile_includes", ["profile_id"])
-    op.create_index("idx_config_profile_includes_included", "config_profile_includes", ["included_profile_id"])
-
-    # Add selected_config_profile_id to tool_instances
-    op.add_column(
-        "tool_instances",
-        sa.Column("selected_config_profile_id", postgresql.UUID(as_uuid=True), sa.ForeignKey("config_profiles.id", ondelete="SET NULL"), nullable=True),
-    )
-    op.create_index("idx_tool_instances_config_profile", "tool_instances", ["selected_config_profile_id"])
-
-
-def downgrade() -> None:
-    # Remove selected_config_profile_id from tool_instances
-    op.drop_index("idx_tool_instances_config_profile", table_name="tool_instances")
-    op.drop_column("tool_instances", "selected_config_profile_id")
-
-    # Drop config_profile_includes table
-    op.drop_index("idx_config_profile_includes_included", table_name="config_profile_includes")
-    op.drop_index("idx_config_profile_includes_profile", table_name="config_profile_includes")
-    op.drop_table("config_profile_includes")
-
-    # Drop config_profiles table
-    op.drop_index("idx_config_profiles_tool_type", table_name="config_profiles")
-    op.drop_index("idx_config_profiles_project", table_name="config_profiles")
-    op.drop_index("idx_config_profiles_user", table_name="config_profiles")
-    op.drop_table("config_profiles")

apps/api/alembic/versions/2026_05_26_add_git_mounts.py

@@ -1,28 +0,0 @@
-"""add_git_mounts_to_config_profiles
-
-Revision ID: 2026_05_26_add_git_mounts
-Revises: f3d2dc90ba3a
-Create Date: 2026-05-26 12:00:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_26_add_git_mounts"
-down_revision: Union[str, Sequence[str], None] = "2026_05_24_220141"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    op.add_column(
-        "config_profiles",
-        sa.Column("git_mounts", sa.JSON(), nullable=True, default=list),
-    )
-
-
-def downgrade() -> None:
-    op.drop_column("config_profiles", "git_mounts")

apps/api/alembic/versions/2026_05_27_external_repos.py

@@ -1,41 +0,0 @@
-"""make_project_id_nullable_in_git_repositories
-
-Revision ID: 2026_05_27_external_repos
-Revises: 2026_05_26_add_git_mounts
-Create Date: 2026-05-27 08:30:00.000000
-
-"""
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_27_external_repos"
-down_revision: Union[str, Sequence[str], None] = "2026_05_26_add_git_mounts"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    # Expand alembic_version version_num to avoid truncation errors
-    op.execute("ALTER TABLE alembic_version ALTER COLUMN version_num TYPE VARCHAR(64)")
-    
-    # Make project_id nullable to allow external repositories
-    op.alter_column(
-        "git_repositories",
-        "project_id",
-        existing_type=sa.UUID(),
-        nullable=True,
-    )
-
-
-def downgrade() -> None:
-    op.alter_column(
-        "git_repositories",
-        "project_id",
-        existing_type=sa.UUID(),
-        nullable=False,
-    )
-    op.execute("ALTER TABLE alembic_version ALTER COLUMN version_num TYPE VARCHAR(32)")

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

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

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

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

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

@@ -1,359 +0,0 @@
-"""add tool definition manifests
-
-Revision ID: 2026_05_28_add_tool_definition_manifests
-Revises: 20260527_160017_add_pi_agent
-Create Date: 2026-05-28T11:00:00
-
-"""
-
-import json
-import uuid
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "2026_05_28_add_tool_definition_manifests"
-down_revision: Union[str, None] = "20260527_160017_add_pi_agent"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-BASE_UBUNTU_ID = uuid.UUID("a1b2c3d4-e5f6-7890-abcd-ef1234567890")
-PI_AGENT_MANIFEST_ID = uuid.UUID("d07b8376-2151-4119-8c1d-27f792aae9a3")
-
-
-def upgrade() -> None:
-    conn = op.get_bind()
-
-    # ── Create tool_definition_manifests table ───────────────────────
-    op.create_table(
-        "tool_definition_manifests",
-        sa.Column("id", sa.UUID(), nullable=False),
-        sa.Column("name", sa.String(64), nullable=False),
-        sa.Column("display_name", sa.String(128), nullable=False),
-        sa.Column("description", sa.Text(), nullable=True),
-        sa.Column("category", sa.String(64), nullable=True),
-        sa.Column("interface_type", sa.String(16), nullable=False),
-        sa.Column("base_image", sa.String(256), nullable=True),
-        sa.Column("base_definition_id", sa.UUID(), nullable=True),
-        sa.Column(
-            "base_version", sa.String(32), nullable=False, server_default="latest"
-        ),
-        sa.Column("manifest", sa.JSON(), nullable=False),
-        sa.Column("dockerfile_cache", sa.Text(), nullable=True),
-        sa.Column("compose_cache", sa.Text(), nullable=True),
-        sa.Column("version", sa.String(32), nullable=False, server_default="v1"),
-        sa.Column("is_base", sa.Boolean(), nullable=False, server_default="false"),
-        sa.Column("created_by_id", sa.UUID(), nullable=True),
-        sa.Column(
-            "created_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
-        ),
-        sa.Column(
-            "updated_at", sa.TIMESTAMP(timezone=True), server_default=sa.func.now()
-        ),
-        sa.PrimaryKeyConstraint("id"),
-        sa.UniqueConstraint("name"),
-        sa.ForeignKeyConstraint(
-            ["base_definition_id"], ["tool_definition_manifests.id"]
-        ),
-        sa.ForeignKeyConstraint(["created_by_id"], ["users.id"]),
-        sa.CheckConstraint(
-            "(base_image IS NOT NULL) OR (base_definition_id IS NOT NULL)",
-            name="ck_tool_definition_manifests_base_required",
-        ),
-    )
-
-    # ── Add columns to tool_types ────────────────────────────────────
-    # Check if manifest_id exists before adding
-    conn = op.get_bind()
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_types' AND column_name = 'manifest_id'
-        """)
-    )
-    if not result.fetchone():
-        op.add_column("tool_types", sa.Column("manifest_id", sa.UUID(), nullable=True))
-        op.create_foreign_key(
-            "fk_tool_types_manifest_id",
-            "tool_types",
-            "tool_definition_manifests",
-            ["manifest_id"],
-            ["id"],
-        )
-
-    # Update definition_type to allow 'legacy' and 'manifest'
-    result = conn.execute(
-        sa.text("""
-            SELECT constraint_name FROM information_schema.check_constraints
-            WHERE constraint_name = 'chk_definition_type'
-        """)
-    )
-    if result.fetchone():
-        op.drop_constraint("chk_definition_type", "tool_types", type_="check")
-
-    op.execute("ALTER TABLE tool_types ALTER COLUMN definition_type TYPE VARCHAR(16)")
-    op.execute(
-        "ALTER TABLE tool_types ALTER COLUMN definition_type SET DEFAULT 'legacy'"
-    )
-
-    # ── Add columns to tool_instances ────────────────────────────────
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_instances' AND column_name = 'manifest_compiled_at'
-        """)
-    )
-    if not result.fetchone():
-        op.add_column(
-            "tool_instances",
-            sa.Column(
-                "manifest_compiled_at", sa.TIMESTAMP(timezone=True), nullable=True
-            ),
-        )
-
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_instances' AND column_name = 'image_tag'
-        """)
-    )
-    if not result.fetchone():
-        op.add_column(
-            "tool_instances",
-            sa.Column("image_tag", sa.String(256), nullable=True),
-        )
-
-    # ── Data migration: create base definition + pi-agent manifest ───
-    conn.execute(
-        sa.text(
-            """
-            INSERT INTO tool_definition_manifests
-            (id, name, display_name, description, interface_type, base_image,
-             manifest, is_base, version, created_at, updated_at)
-            VALUES
-            (:base_id, 'ubuntu-24.04-dev', 'Ubuntu 24.04 Dev Base',
-             'Base development environment with build tools', 'terminal',
-             'ubuntu:24.04', :base_manifest, true, 'v1', now(), now())
-        """
-        ),
-        {
-            "base_id": BASE_UBUNTU_ID,
-            "base_manifest": json.dumps(
-                {
-                    "name": "ubuntu-24.04-dev",
-                    "display_name": "Ubuntu 24.04 Dev Base",
-                    "interface_type": "terminal",
-                    "base_image": "ubuntu:24.04",
-                    "packages": {
-                        "apt": [
-                            "curl",
-                            "wget",
-                            "git",
-                            "build-essential",
-                            "ca-certificates",
-                            "python3",
-                            "python3-pip",
-                        ]
-                    },
-                    "user": {
-                        "name": "user",
-                        "uid": 1000,
-                        "gid": 1000,
-                        "create_home": True,
-                        "shell": "/bin/bash",
-                    },
-                    "env": {"DEBIAN_FRONTEND": "noninteractive"},
-                }
-            ),
-        },
-    )
-
-    conn.execute(
-        sa.text(
-            """
-            INSERT INTO tool_definition_manifests
-            (id, name, display_name, description, category, interface_type,
-             base_definition_id, base_version, manifest, version, created_at, updated_at)
-            VALUES
-            (:manifest_id, 'pi-agent', 'Pi Agent',
-             'Terminal-based coding harness with nvim, ranger, tmux',
-             'development', 'terminal', :base_id, 'v1', :manifest, 'v1',
-             now(), now())
-        """
-        ),
-        {
-            "manifest_id": PI_AGENT_MANIFEST_ID,
-            "base_id": BASE_UBUNTU_ID,
-            "manifest": json.dumps(
-                {
-                    "name": "pi-agent",
-                    "display_name": "Pi Agent",
-                    "description": "Terminal-based coding harness",
-                    "category": "development",
-                    "interface_type": "terminal",
-                    "base_definition_id": str(BASE_UBUNTU_ID),
-                    "base_version": "v1",
-                    "packages": {
-                        "apt": [
-                            "neovim",
-                            "ranger",
-                            "tmux",
-                            "htop",
-                            "tree",
-                            "jq",
-                        ],
-                        "node": {"version": "20"},
-                        "npm_global": ["@earendil-works/pi-coding-agent"],
-                    },
-                    "user": {
-                        "name": "user",
-                        "uid": 1001,
-                        "gid": 1001,
-                        "create_home": True,
-                        "shell": "/bin/bash",
-                    },
-                    "env": {"DEBIAN_FRONTEND": "noninteractive"},
-                    "scripts": {
-                        "build": [
-                            "git config --global init.defaultBranch main && git config --global user.email 'dev@headquarter.local' && git config --global user.name 'Developer'",
-                            "mkdir -p /home/user/.config/ranger && echo 'set preview_files true' > /home/user/.config/ranger/rc.conf",
-                        ],
-                        "startup": [
-                            "if [ -d /workspace ]; then sudo chown -R user:user /workspace 2>/dev/null || true; fi",
-                        ],
-                    },
-                    "mounts": [
-                        {
-                            "name": "workspace",
-                            "target": "/workspace",
-                            "source_type": "repo",
-                            "writable": True,
-                            "owner": "user",
-                        },
-                    ],
-                    "runtime": {
-                        "command": ["/bin/bash"],
-                        "stdin_open": True,
-                        "tty": True,
-                        "working_dir": "/workspace",
-                    },
-                }
-            ),
-        },
-    )
-
-    # ── Update existing pi-agent tool_type ───────────────────────────
-    conn.execute(
-        sa.text(
-            """
-            UPDATE tool_types
-            SET manifest_id = :manifest_id,
-                definition_type = 'manifest',
-                dockerfile_template = NULL,
-                compose_template = NULL
-            WHERE name = 'pi-agent'
-        """
-        ),
-        {"manifest_id": PI_AGENT_MANIFEST_ID},
-    )
-
-
-def downgrade() -> None:
-    conn = op.get_bind()
-
-    # Restore pi-agent templates if manifest_id column exists
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_types' AND column_name = 'manifest_id'
-        """)
-    )
-    has_manifest_id = result.fetchone() is not None
-
-    if has_manifest_id:
-        conn.execute(
-            sa.text(
-                """
-                UPDATE tool_types
-                SET manifest_id = NULL,
-                    definition_type = 'dockerfile',
-                    dockerfile_template = :dockerfile,
-                    compose_template = :compose
-                WHERE name = 'pi-agent'
-            """
-            ),
-            {
-                "dockerfile": """# Pi Coding Agent - Terminal-based coding harness
-FROM ubuntu:24.04
-
-ENV DEBIAN_FRONTEND=noninteractive
-
-RUN apt-get update && apt-get install -y \\
-    curl wget git neovim ranger tmux htop tree jq \\
-    ca-certificates python3 python3-pip build-essential \\
-    && rm -rf /var/lib/apt/lists/*
-
-RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \\
-    && apt-get install -y nodejs \\
-    && rm -rf /var/lib/apt/lists/*
-
-RUN npm install -g --ignore-scripts @earendil-works/pi-coding-agent
-
-RUN useradd -m -s /bin/bash user
-WORKDIR /home/user
-
-RUN git config --global init.defaultBranch main \\
-    && git config --global user.email "dev@headquarter.local" \\
-    && git config --global user.name "Developer"
-
-RUN printf '%s\\n' 'set -g mouse on' 'set -g default-terminal "screen-256color"' > /home/user/.tmux.conf
-
-RUN mkdir -p /home/user/.config/ranger \\
-    && printf '%s\\n' 'set preview_files true' 'set use_preview_script true' > /home/user/.config/ranger/rc.conf
-
-RUN mkdir -p /home/user/.pi/agent
-
-USER user
-
-CMD ["/bin/bash"]
-""",
-                "compose": """services:
-  app:
-    build: .
-    stdin_open: true
-    tty: true
-    volumes:
-      - ${REPO_PATH}:/workspace
-    working_dir: /workspace
-    command: /bin/bash""",
-            },
-        )
-
-    # Drop columns conditionally
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_instances' AND column_name = 'image_tag'
-        """)
-    )
-    if result.fetchone():
-        op.drop_column("tool_instances", "image_tag")
-
-    result = conn.execute(
-        sa.text("""
-            SELECT column_name FROM information_schema.columns
-            WHERE table_name = 'tool_instances' AND column_name = 'manifest_compiled_at'
-        """)
-    )
-    if result.fetchone():
-        op.drop_column("tool_instances", "manifest_compiled_at")
-
-    if has_manifest_id:
-        op.drop_constraint(
-            "fk_tool_types_manifest_id", "tool_types", type_="foreignkey"
-        )
-        op.drop_column("tool_types", "manifest_id")
-
-    op.drop_table("tool_definition_manifests")

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

apps/api/alembic/versions/6fc7bfcf199f_merge_remove_is_builtin_and_add_config_.py

@@ -1,23 +0,0 @@
-"""merge_remove_is_builtin_and_add_config_profiles
-
-Revision ID: 6fc7bfcf199f
-Revises: 2026_05_23_remove_is_builtin, 2026_05_24_add_config_profiles
-Create Date: 2026-05-24 18:00:43.990361
-"""
-
-
-
-
-# revision identifiers, used by Alembic.
-revision = '6fc7bfcf199f'
-down_revision = ('2026_05_23_remove_is_builtin', '2026_05_24_add_config_profiles')
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    pass
-
-
-def downgrade() -> None:
-    pass

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

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

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

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

apps/api/alembic/versions/f3d2dc90ba3a_merge_single_interface_and_clone_mode.py

@@ -1,23 +0,0 @@
-"""merge_single_interface_and_clone_mode
-
-Revision ID: f3d2dc90ba3a
-Revises: 0015_single_interface, 2026_05_22_add_clone_mode
-Create Date: 2026-05-24 10:43:14.000000
-
-"""
-from typing import Sequence, Union
-
-
-# revision identifiers, used by Alembic.
-revision: str = "f3d2dc90ba3a"
-down_revision: Union[str, Sequence[str], None] = ("0015_single_interface", "2026_05_22_add_clone_mode")
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    pass
-
-
-def downgrade() -> None:
-    pass

apps/api/alembic/versions/fc8f1a20cbf6_merge_home_directory_and_pi_agent_mount_.py

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

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

@@ -1,51 +0,0 @@
-# apps/api/src (index)
-dir: apps/api/src
-
-## role
-Core backend API package for the "Headquarter API" FastAPI application, handling configuration, database setup, logging, and application bootstrap.
-## 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/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/models/.pi-map.index.md
-## dirty
--

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

@@ -1,35 +0,0 @@
-# apps/api/src
-dir: apps/api/src
-
-index: apps/api/src/.pi-map.index.md
-
-## role
-Core backend API package for the "Headquarter API" FastAPI application, handling configuration, database setup, logging, and application bootstrap.
-## files
-- __init__.py | Marks the directory as a Python package for the Headquarter API.
-- config.py | Defines application configuration settings with environment variable loading, database URL construction, and computed properties for service URLs and security settings. | exp: class:Settings, func:build_database_url(user: str, password: str, host: str, port: int, database: str) → str | dep: pydantic, pydantic_settings
-- database.py | Sets up an async SQLAlchemy database engine with retry logic and runs Alembic migrations via subprocess to initialize the database. | exp: func:init_database(max_retries, retry_delay) → bool, call:range, call:engine.connect, call:test_conn.execute, call:text, call:test_conn.close, call:logger.info, call:asyncio.get_event_loop().run_in_executor, call:subprocess.run, call:os.path.dirname, call:os.path.abspath, call:logger.debug, call:logger.error, call:asyncio.sleep, call:str(exc).lower, call:logger.warning | dep: asyncio, logging, os, subprocess, sqlalchemy.ext.asyncio, sqlalchemy.pool, src.config, sqlalchemy
-- logging_config.py | Configures structured JSON logging with correlation ID injection, request/response logging middleware, and exception handling 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, starlette
-- main.py | Bootstraps a FastAPI application called "Headquarter API" with database initialization, health monitoring, CORS, logging middleware, and modular API routers. | exp: func:_sanitize_validation_errors(errors), call:error.get, call:str, call:ctx.items, call:isinstance, call:type, call:sanitized.append, func:validation_exception_handler(request: Request, exc: RequestValidationError), call:exc.errors, call:logger.warning, call:_sanitize_validation_errors, call:JSONResponse, func:on_startup(), call:logger.info, call:init_database, call:logger.error, call:sys.exit, call:_health_monitor.start, call:seed_builtin_tool_types, func:on_shutdown(), call:logger.info, call:_health_monitor.stop | dep: logging, os, fastapi, fastapi.exceptions, fastapi.middleware.cors, fastapi.responses, fastapi.staticfiles, src.api.config, src.api.project, src.api.system, src.api.tool, src.api.user, src.api.workspace, src.config, src.models, src.database, src.logging_config, src.seeds.builtin_tool_types, src.services.instance, src.services.shared, sys, src.api
-## arch
-Layered architecture with separation of concerns across config (settings/env), database (async SQLAlchemy with Alembic migrations), logging (structured JSON with middleware), and main (app composition with modular routers and health monitoring).
-## tags
-src, logging, database, api, call:logger.info, 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/models/.pi-map.index.md
-## dirty
--

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

@@ -1,40 +0,0 @@
-# apps/api/src/api (index)
-dir: apps/api/src/api
-
-## role
-Provides shared Pydantic validators and package initialization for API schema validation across the API layer.
-## parent
-index: apps/api/src/.pi-map.index.md
-map: apps/api/src/.pi-map.md
-## children
-- apps/api/src/api/config
-  index: apps/api/src/api/config/.pi-map.index.md
-  map: apps/api/src/api/config/.pi-map.md
-- apps/api/src/api/project
-  index: apps/api/src/api/project/.pi-map.index.md
-  map: apps/api/src/api/project/.pi-map.md
-- apps/api/src/api/system
-  index: apps/api/src/api/system/.pi-map.index.md
-  map: apps/api/src/api/system/.pi-map.md
-- apps/api/src/api/tool
-  index: apps/api/src/api/tool/.pi-map.index.md
-  map: apps/api/src/api/tool/.pi-map.md
-- apps/api/src/api/user
-  index: apps/api/src/api/user/.pi-map.index.md
-  map: apps/api/src/api/user/.pi-map.md
-- apps/api/src/api/workspace
-  index: apps/api/src/api/workspace/.pi-map.index.md
-  map: apps/api/src/api/workspace/.pi-map.md
-## files
-- __init__.py
-- shared_validators.py
-## links
-index: apps/api/src/api/.pi-map.index.md
-map: apps/api/src/api/.pi-map.md
-## workflows
-- change api behavior
-  read: __init__.py, shared_validators.py
-- explore api subdirectories
-  index: apps/api/src/api/config/.pi-map.index.md, apps/api/src/api/project/.pi-map.index.md, apps/api/src/api/system/.pi-map.index.md
-## dirty
--

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

@@ -1,30 +0,0 @@
-# apps/api/src/api
-dir: apps/api/src/api
-
-index: apps/api/src/api/.pi-map.index.md
-
-## role
-Provides shared Pydantic validators and package initialization for API schema validation across the API layer.
-## files
-- __init__.py | Marks the directory as a Python package for API routers.
-- shared_validators.py | Provides reusable Pydantic validators for API schema fields including mount paths, file dictionaries, 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
-Utility module pattern with reusable cross-cutting Pydantic validators for common API field types (mount paths, files, env vars, volumes).
-## tags
-validate, raise:value, error, call:isinstance, validators, mount, api, init
-## 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
--

apps/api/src/api/__init__.py

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

apps/api/src/api/auth.py

@@ -48,7 +48,7 @@ async def login(next: str = "/") -> RedirectResponse:
         redirect_uri=redirect_uri,
         state=state,
     )
-    logger.debug("Auth login initiated: redirect_uri=%s, next=%s", redirect_uri, next)
+    logger.info("Auth login initiated: redirect_uri=%s, next=%s", redirect_uri, next)
     response = RedirectResponse(location)
     response.set_cookie("auth_state", state, httponly=True, samesite="lax")
     response.set_cookie("auth_next", next, httponly=True, samesite="lax")
@@ -63,7 +63,7 @@ async def callback(
     auth_next: str | None = Cookie(default="/"),
     session: AsyncSession = Depends(get_db_session),
 ) -> RedirectResponse:
-    logger.debug("Auth callback received: code=%s... state=%s", code[:10] if code else "None", state[:10] if state else "None")
+    logger.info("Auth callback received: code=%s... state=%s", code[:10] if code else "None", state[:10] if state else "None")
     
     if auth_state is None or auth_state != state:
         logger.warning("State mismatch: cookie=%s, param=%s", auth_state, state)
@@ -71,7 +71,7 @@ async def callback(
 
     settings = Settings()
     redirect_uri = f"{settings.api_base_url}/auth/callback"
-    logger.debug("Exchanging code for tokens (redirect_uri=%s)", redirect_uri)
+    logger.info("Exchanging code for tokens (redirect_uri=%s)", redirect_uri)
     
     async with httpx.AsyncClient() as client:
         try:
@@ -92,7 +92,7 @@ async def callback(
                 access_token=token_payload["access_token"],
                 client=client,
             )
-            logger.debug("User info fetched successfully")
+            logger.info("User info fetched successfully")
         except Exception as exc:
             logger.error("User info fetch failed: %s", exc)
             raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="failed to fetch user info")
@@ -100,19 +100,19 @@ async def callback(
     authentik_id = str(user_info.get("sub", ""))
     email = str(user_info.get("email", f"{authentik_id}@authentik.local"))
     name = str(user_info.get("name", email))
-    logger.debug("User info: authentik_id=%s, email=%s, name=%s", authentik_id, email, name)
+    logger.info("User info: authentik_id=%s, email=%s, name=%s", authentik_id, email, name)
 
     try:
         user = await session.scalar(select(User).where(User.authentik_id == authentik_id))
         if user is None:
-            logger.debug("Creating new user: authentik_id=%s", authentik_id)
+            logger.info("Creating new user: authentik_id=%s", authentik_id)
             user = User(email=email, name=name, authentik_id=authentik_id, avatar_url=None)
             session.add(user)
             await session.commit()
             await session.refresh(user)
             logger.info("New user created: id=%s", user.id)
         else:
-            logger.debug("Existing user found: id=%s, updating info", user.id)
+            logger.info("Existing user found: id=%s, updating info", user.id)
             user.email = email
             user.name = name
             await session.commit()
@@ -165,20 +165,20 @@ async def me(
     session_cookie: str | None = Cookie(default=None, alias="session"),
     session: AsyncSession = Depends(get_db_session),
 ) -> dict[str, Any]:
-    logger.debug("Auth /me called, cookie present: %s", bool(session_cookie))
+    logger.info("Auth /me called, cookie present: %s", bool(session_cookie))
     
     if not session_cookie:
         logger.warning("Auth /me: missing session cookie")
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="missing session")
 
     settings = Settings()
-    logger.debug("Auth /me: cookie_domain=%s, cookie_secure=%s, cookie_samesite=%s", 
+    logger.info("Auth /me: cookie_domain=%s, cookie_secure=%s, cookie_samesite=%s", 
                 settings.cookie_domain, settings.cookie_secure, settings.cookie_samesite)
     
     try:
         payload = decode_session_cookie(settings=settings, cookie_value=session_cookie)
         user_id = payload["user_id"]
-        logger.debug("Auth /me: decoded session for user_id=%s", user_id)
+        logger.info("Auth /me: decoded session for user_id=%s", user_id)
     except ValueError as exc:
         logger.warning("Auth /me: invalid session: %s", exc)
         raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail=str(exc))

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

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

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

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

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

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

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

@@ -1,300 +0,0 @@
-"""Config profile API endpoints."""
-
-import logging
-import uuid
-
-from fastapi import APIRouter, Depends, HTTPException, Query, status
-from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession
-from sqlalchemy.orm import selectinload
-
-from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models import ConfigProfile, ConfigProfileInclude, UserConfig
-from src.schemas.config import (
-    ConfigProfileCreate,
-    ConfigProfileIncludeUpdate,
-    ConfigProfileResponse,
-    ConfigProfileUpdate,
-    DefaultProfilesUpdate,
-    ValidateGitUrlRequest,
-    ValidateGitUrlResponse,
-)
-from src.services.config.config_profile_resolver import (
-    ConfigProfileCycleError,
-    resolve_profile,
-    resolved_profile_to_dict,
-)
-from src.services.config.crud_service import (
-    create_profile,
-    get_or_create_user_config,
-    get_profile_with_includes,
-    profile_to_response,
-    update_includes,
-    update_profile,
-    validate_default_profiles,
-)
-from src.services.config.resolver_service import (
-    resolve_default_profile,
-    validate_git_url,
-)
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
-
-
-@router.get("", response_model=list[ConfigProfileResponse])
-async def list_config_profiles(
-    project_id: str | None = Query(None, description="Filter by project compatibility"),
-    tool_type_id: str | None = Query(
-        None, description="Filter by tool type compatibility"
-    ),
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """List config profiles, optionally filtered by compatibility."""
-    user_uuid = current_user_id
-    query = (
-        select(ConfigProfile)
-        .where(ConfigProfile.user_id == user_uuid)
-        .options(selectinload(ConfigProfile.includes))
-    )
-
-    if project_id or tool_type_id:
-        from sqlalchemy import or_
-
-        project_uuid = uuid.UUID(project_id) if project_id else None
-        tool_uuid = uuid.UUID(tool_type_id) if tool_type_id else None
-
-        conditions: list = []
-        conditions.append(
-            (ConfigProfile.project_id.is_(None))
-            & (ConfigProfile.tool_type_id.is_(None))
-        )
-        if project_uuid:
-            conditions.append(ConfigProfile.project_id == project_uuid)
-        if tool_uuid:
-            conditions.append(ConfigProfile.tool_type_id == tool_uuid)
-        if project_uuid and tool_uuid:
-            conditions.append(
-                (ConfigProfile.project_id == project_uuid)
-                & (ConfigProfile.tool_type_id == tool_uuid)
-            )
-
-        query = query.where(or_(*conditions))
-
-    result = await session.execute(query)
-    profiles = result.scalars().all()
-    return [profile_to_response(p) for p in profiles]
-
-
-@router.post(
-    "", response_model=ConfigProfileResponse, status_code=status.HTTP_201_CREATED
-)
-async def create_config_profile(
-    data: ConfigProfileCreate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Create a new config profile."""
-    profile = await create_profile(session, current_user_id, data)
-    logger.debug("Created config profile %s for user %s", profile.id, current_user_id)
-    return profile_to_response(profile)
-
-
-@router.get("/{profile_id}", response_model=ConfigProfileResponse)
-async def get_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Get a config profile by ID."""
-    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
-        )
-    if profile.user_id != current_user_id:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
-        )
-    return profile_to_response(profile)
-
-
-@router.put("/{profile_id}", response_model=ConfigProfileResponse)
-async def update_config_profile(
-    profile_id: str,
-    data: ConfigProfileUpdate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Update a config profile."""
-    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
-        )
-    if profile.user_id != current_user_id:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
-        )
-
-    profile = await update_profile(session, profile, data)
-    logger.debug("Updated config profile %s", profile.id)
-    return profile_to_response(profile)
-
-
-@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
-async def delete_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Delete a config profile."""
-    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
-        )
-    if profile.user_id != current_user_id:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
-        )
-
-    await session.delete(profile)
-    await session.commit()
-
-    logger.debug("Deleted config profile %s", profile_id)
-    return None
-
-
-@router.put("/{profile_id}/includes", response_model=ConfigProfileResponse)
-async def update_profile_includes_endpoint(
-    profile_id: str,
-    data: ConfigProfileIncludeUpdate,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Update the ordered includes for a config profile."""
-    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
-        )
-    if profile.user_id != current_user_id:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
-        )
-
-    included_uuids = [uuid.UUID(inc_id) for inc_id in data.includes]
-    profile = await update_includes(session, profile, included_uuids, current_user_id)
-
-    inc_result = await session.execute(
-        select(ConfigProfileInclude).where(
-            ConfigProfileInclude.profile_id == profile.id
-        )
-    )
-    direct_includes = inc_result.scalars().all()
-
-    logger.debug("Updated includes for config profile %s", profile.id)
-    return profile_to_response(profile, list(direct_includes))
-
-
-@router.get("/{profile_id}/preview")
-async def preview_config_profile(
-    profile_id: str,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Preview the resolved output of a config profile."""
-    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
-    if profile is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
-        )
-    if profile.user_id != current_user_id:
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
-        )
-
-    try:
-        resolved = await resolve_profile(session, profile.id)
-    except ConfigProfileCycleError as exc:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=str(exc),
-        )
-
-    return resolved_profile_to_dict(resolved)
-
-
-@router.get("/defaults/resolve")
-async def resolve_default_profile_endpoint(
-    project_id: str = Query(..., description="Project ID"),
-    tool_type_id: str = Query(..., description="Tool type ID"),
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-):
-    """Resolve the default config profile for a project/tool combination."""
-    return await resolve_default_profile(
-        session,
-        current_user_id,
-        uuid.UUID(project_id),
-        uuid.UUID(tool_type_id),
-    )
-
-
-@router.get("/defaults")
-async def get_default_profiles_endpoint(
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get all default profile mappings for the current user."""
-    result = await session.execute(
-        select(UserConfig).where(UserConfig.user_id == user_id)
-    )
-    user_config = result.scalar_one_or_none()
-    return {"default_profiles": user_config.default_profiles if user_config else {}}
-
-
-@router.put("/defaults")
-async def set_default_profiles_endpoint(
-    data: DefaultProfilesUpdate,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Set default profile mappings for the current user."""
-    await validate_default_profiles(session, user_id, data.default_profiles)
-    user_config = await get_or_create_user_config(session, user_id)
-    user_config.config = {
-        **user_config.config,
-        "default_profiles": data.default_profiles,
-    }
-    await session.commit()
-    await session.refresh(user_config)
-    return {"default_profiles": user_config.default_profiles}
-
-
-@router.get("/defaults/{tool_type_id}")
-async def get_default_profile_for_tool_type_endpoint(
-    tool_type_id: str,
-    user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> dict:
-    """Get the default profile ID for a specific tool type."""
-    result = await session.execute(
-        select(UserConfig).where(UserConfig.user_id == user_id)
-    )
-    user_config = result.scalar_one_or_none()
-    profile_id = user_config.default_profiles.get(tool_type_id) if user_config else None
-    return {"tool_type_id": tool_type_id, "profile_id": profile_id}
-
-
-@router.post("/validate-git-url", response_model=ValidateGitUrlResponse)
-async def validate_git_url_endpoint(
-    data: ValidateGitUrlRequest,
-    current_user_id: uuid.UUID = Depends(get_current_user_id),
-    session: AsyncSession = Depends(get_db_session),
-) -> ValidateGitUrlResponse:
-    """Validate a git remote URL and list available branches."""
-    return await validate_git_url(session, current_user_id, data.url, data.ssh_key_id)

apps/api/src/api/config_folders.py

@@ -0,0 +1,284 @@
+"""Config folder API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from pydantic import Field
+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.config_folder import ConfigFolder
+from src.schemas.config_folder import (
+    ConfigFolderCreate,
+    ConfigFolderUpdate,
+    ConfigFolderResponse,
+    ProjectOverrideCreate,
+)
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/config-folders", tags=["config-folders"])
+
+
+@router.get("", summary="List config folders", description="Get all config folders for the current user.")
+async def list_config_folders(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """List config folders for the current user."""
+    query = select(ConfigFolder).where(ConfigFolder.user_id == user_id)
+    result = await session.execute(query)
+    folders = result.scalars().all()
+    
+    return {
+        "folders": [
+            {
+                "id": str(f.id),
+                "user_id": str(f.user_id),
+                "name": f.name,
+                "description": f.description,
+                "mount_path": f.mount_path,
+                "files": f.files,
+                "project_overrides": f.project_overrides,
+                "is_active": f.is_active,
+                "created_at": f.created_at.isoformat() if f.created_at else None,
+                "updated_at": f.updated_at.isoformat() if f.updated_at else None,
+            }
+            for f in folders
+        ]
+    }
+
+
+@router.post("", summary="Create config folder", description="Create a new config folder.", status_code=status.HTTP_201_CREATED)
+async def create_config_folder(
+    data: ConfigFolderCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Create a config folder."""
+    # Check for duplicate name
+    existing = await session.scalar(
+        select(ConfigFolder).where(
+            ConfigFolder.user_id == user_id,
+            ConfigFolder.name == data.name,
+        )
+    )
+    if existing:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail=f"config folder with name '{data.name}' already exists"
+        )
+    
+    folder = ConfigFolder(
+        user_id=user_id,
+        name=data.name,
+        description=data.description,
+        mount_path=data.mount_path,
+        files=data.files,
+    )
+    session.add(folder)
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.put("/{folder_id}", summary="Update config folder", description="Update an existing config folder.")
+async def update_config_folder(
+    folder_id: uuid.UUID,
+    data: ConfigFolderUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    if data.name is not None:
+        folder.name = data.name
+    if data.description is not None:
+        folder.description = data.description
+    if data.mount_path is not None:
+        folder.mount_path = data.mount_path
+    if data.files is not None:
+        folder.files = data.files
+    if data.is_active is not None:
+        folder.is_active = data.is_active
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.delete("/{folder_id}", summary="Delete config folder", description="Delete a config folder.", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_folder(
+    folder_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Delete a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    await session.delete(folder)
+    await session.commit()
+
+
+class ProjectOverrideWithId(ProjectOverrideCreate):
+    project_id: uuid.UUID = Field(description="Project ID for the override")
+
+
+@router.get("/{folder_id}", summary="Get config folder by ID", description="Get a single config folder by its ID.")
+async def get_config_folder(
+    folder_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Get a config folder by ID."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    return {
+        "id": str(folder.id),
+        "user_id": str(folder.user_id),
+        "name": folder.name,
+        "description": folder.description,
+        "mount_path": folder.mount_path,
+        "files": folder.files,
+        "project_overrides": folder.project_overrides,
+        "is_active": folder.is_active,
+        "created_at": folder.created_at.isoformat() if folder.created_at else None,
+        "updated_at": folder.updated_at.isoformat() if folder.updated_at else None,
+    }
+
+
+@router.post("/{folder_id}/overrides", summary="Add project override", description="Add a project override to a config folder.")
+async def add_project_override(
+    folder_id: uuid.UUID,
+    data: ProjectOverrideWithId,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Add a project override to a config folder."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Initialize project_overrides if None
+    if folder.project_overrides is None:
+        folder.project_overrides = {}
+    
+    # Add/update override
+    override_data = {}
+    if data.mount_path is not None:
+        override_data["mount_path"] = data.mount_path
+    if data.files is not None:
+        override_data["files"] = data.files
+    
+    # Use a copy to trigger SQLAlchemy change detection on JSONB
+    current_overrides = dict(folder.project_overrides or {})
+    current_overrides[str(data.project_id)] = override_data
+    folder.project_overrides = current_overrides
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides,
+    }
+
+
+@router.put("/{folder_id}/overrides/{project_id}", summary="Update project override", description="Update a project override.")
+async def update_project_override(
+    folder_id: uuid.UUID,
+    project_id: uuid.UUID,
+    data: ProjectOverrideCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    """Update a project override."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Initialize project_overrides if None
+    if folder.project_overrides is None:
+        folder.project_overrides = {}
+    
+    # Update override
+    current_overrides = dict(folder.project_overrides or {})
+    override_data = current_overrides.get(str(project_id), {})
+    if data.mount_path is not None:
+        override_data["mount_path"] = data.mount_path
+    if data.files is not None:
+        override_data["files"] = data.files
+    
+    current_overrides[str(project_id)] = override_data
+    folder.project_overrides = current_overrides
+    
+    # Mark the field as modified to ensure SQLAlchemy detects the change
+    from sqlalchemy.orm.attributes import flag_modified
+    flag_modified(folder, "project_overrides")
+    
+    await session.commit()
+    await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides,
+    }
+
+
+@router.delete("/{folder_id}/overrides/{project_id}", summary="Remove project override", description="Remove a project override.")
+async def remove_project_override(
+    folder_id: uuid.UUID,
+    project_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    """Remove a project override."""
+    folder = await session.get(ConfigFolder, folder_id)
+    if folder is None or folder.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config folder not found")
+    
+    # Remove override if exists
+    current_overrides = dict(folder.project_overrides or {})
+    if str(project_id) in current_overrides:
+        del current_overrides[str(project_id)]
+        folder.project_overrides = current_overrides
+        await session.commit()
+        await session.refresh(folder)
+    
+    return {
+        "id": str(folder.id),
+        "project_overrides": folder.project_overrides or {},
+    }

apps/api/src/api/config_profiles.py

@@ -0,0 +1,299 @@
+"""Config profile API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.orm import selectinload
+
+from src.auth.dependencies import get_current_user_id, get_db_session
+from src.models.config_include import ConfigInclude
+from src.models.config_mount import ConfigMount
+from src.models.config_profile import ConfigProfile
+from src.models.tool_type import ToolType
+from src.models.user_config import UserConfig
+from src.schemas.config_profile import (
+    ConfigIncludeCreate,
+    ConfigIncludeUpdate,
+    ConfigMountCreate,
+    ConfigMountUpdate,
+    ConfigProfileCreate,
+    ConfigProfileUpdate,
+    DefaultProfilesUpdate,
+)
+from src.services.config_profiles import (
+    check_duplicate_include,
+    check_duplicate_mount_path,
+    check_duplicate_name,
+    get_default_profile_for_tool_type,
+    get_default_profiles,
+    get_owned_profile,
+    include_to_dict,
+    list_includes_for_profile,
+    list_mounts_for_profile,
+    mount_to_dict,
+    profile_to_dict,
+    set_default_profiles,
+    validate_includes_no_cycle,
+)
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
+
+
+
+@router.get("")
+async def list_config_profiles(
+    tool_type_id: str | None = None,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    query = select(ConfigProfile).where(ConfigProfile.user_id == user_id)
+    if tool_type_id:
+        tool_type = await session.get(ToolType, uuid.UUID(tool_type_id))
+        if tool_type is None:
+            raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="tool type not found")
+    result = await session.execute(query.order_by(ConfigProfile.name))
+    return {"profiles": [profile_to_dict(p) for p in result.scalars().all()]}
+
+
+@router.post("", status_code=status.HTTP_201_CREATED)
+async def create_config_profile(
+    data: ConfigProfileCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    await check_duplicate_name(session, user_id, data.name)
+    profile = ConfigProfile(user_id=user_id, name=data.name, description=data.description)
+    session.add(profile)
+    await session.commit()
+    await session.refresh(profile)
+    return profile_to_dict(profile)
+
+
+@router.get("/defaults")
+async def get_default_profiles_endpoint(
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    return await get_default_profiles(session, user_id)
+
+
+@router.put("/defaults")
+async def set_default_profiles_endpoint(
+    data: DefaultProfilesUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    return await set_default_profiles(session, user_id, data.default_profiles)
+
+
+@router.get("/defaults/{tool_type_id}")
+async def get_default_profile_for_tool_type_endpoint(
+    tool_type_id: str,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    return await get_default_profile_for_tool_type(session, user_id, tool_type_id)
+
+
+@router.get("/{profile_id}")
+async def get_config_profile(
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    profile = await session.get(
+        ConfigProfile,
+        profile_id,
+        options=[selectinload(ConfigProfile.includes), selectinload(ConfigProfile.mounts)],
+    )
+    if profile is None or profile.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="config profile not found")
+    includes_data = []
+    for inc in profile.includes:
+        included_profile = await session.get(ConfigProfile, inc.included_profile_id)
+        includes_data.append(include_to_dict(inc, included_profile.name if included_profile else None))
+    return {
+        **profile_to_dict(profile),
+        "includes": includes_data,
+        "mounts": [mount_to_dict(m) for m in profile.mounts],
+    }
+
+
+@router.put("/{profile_id}")
+async def update_config_profile(
+    profile_id: uuid.UUID,
+    data: ConfigProfileUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    profile = await get_owned_profile(profile_id, user_id, session)
+    if data.name is not None:
+        await check_duplicate_name(session, user_id, data.name, exclude_id=profile_id)
+        profile.name = data.name
+    if data.description is not None:
+        profile.description = data.description
+    await session.commit()
+    await session.refresh(profile)
+    return profile_to_dict(profile)
+
+
+@router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_config_profile(
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    profile = await get_owned_profile(profile_id, user_id, session)
+    await session.delete(profile)
+    await session.commit()
+
+
+
+@router.get("/{profile_id}/includes")
+async def list_profile_includes(
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    await get_owned_profile(profile_id, user_id, session)
+    return await list_includes_for_profile(session, profile_id)
+
+
+@router.post("/{profile_id}/includes", status_code=status.HTTP_201_CREATED)
+async def add_profile_include(
+    profile_id: uuid.UUID,
+    data: ConfigIncludeCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    profile = await get_owned_profile(profile_id, user_id, session)
+    included_profile_id = uuid.UUID(data.included_profile_id)
+    if included_profile_id == profile_id:
+        raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="a profile cannot include itself")
+    included_profile = await session.get(ConfigProfile, included_profile_id)
+    if included_profile is None:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="included profile not found")
+    if included_profile.user_id != user_id:
+        raise HTTPException(status_code=status.HTTP_403_FORBIDDEN, detail="included profile does not belong to user")
+    await check_duplicate_include(session, profile_id, included_profile_id)
+    await validate_includes_no_cycle(session, profile_id, included_profile_id)
+    include = ConfigInclude(
+        profile_id=profile_id,
+        included_profile_id=included_profile_id,
+        order_index=data.order_index,
+    )
+    session.add(include)
+    await session.commit()
+    await session.refresh(include)
+    return include_to_dict(include, included_profile.name)
+
+
+@router.put("/{profile_id}/includes/{include_id}")
+async def update_profile_include(
+    profile_id: uuid.UUID,
+    include_id: uuid.UUID,
+    data: ConfigIncludeUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    await get_owned_profile(profile_id, user_id, session)
+    include = await session.get(ConfigInclude, include_id)
+    if include is None or include.profile_id != profile_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="include not found")
+    include.order_index = data.order_index
+    await session.commit()
+    await session.refresh(include)
+    included_profile = await session.get(ConfigProfile, include.included_profile_id)
+    return include_to_dict(include, included_profile.name if included_profile else None)
+
+
+@router.delete("/{profile_id}/includes/{include_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def remove_profile_include(
+    profile_id: uuid.UUID,
+    include_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    await get_owned_profile(profile_id, user_id, session)
+    include = await session.get(ConfigInclude, include_id)
+    if include is None or include.profile_id != profile_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="include not found")
+    await session.delete(include)
+    await session.commit()
+
+
+
+@router.get("/{profile_id}/mounts")
+async def list_profile_mounts(
+    profile_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    await get_owned_profile(profile_id, user_id, session)
+    return await list_mounts_for_profile(session, profile_id)
+
+
+@router.post("/{profile_id}/mounts", status_code=status.HTTP_201_CREATED)
+async def add_profile_mount(
+    profile_id: uuid.UUID,
+    data: ConfigMountCreate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    profile = await get_owned_profile(profile_id, user_id, session)
+    await check_duplicate_mount_path(session, profile_id, data.target_path)
+    mount = ConfigMount(
+        profile_id=profile_id,
+        target_path=data.target_path,
+        mode=data.mode,
+        files=data.files,
+        order_index=data.order_index,
+    )
+    session.add(mount)
+    await session.commit()
+    await session.refresh(mount)
+    return mount_to_dict(mount)
+
+
+@router.put("/{profile_id}/mounts/{mount_id}")
+async def update_profile_mount(
+    profile_id: uuid.UUID,
+    mount_id: uuid.UUID,
+    data: ConfigMountUpdate,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    await get_owned_profile(profile_id, user_id, session)
+    mount = await session.get(ConfigMount, mount_id)
+    if mount is None or mount.profile_id != profile_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="mount not found")
+    if data.target_path is not None:
+        await check_duplicate_mount_path(session, profile_id, data.target_path, exclude_id=mount_id)
+        mount.target_path = data.target_path
+    if data.files is not None:
+        mount.files = data.files
+    if data.order_index is not None:
+        mount.order_index = data.order_index
+    await session.commit()
+    await session.refresh(mount)
+    return mount_to_dict(mount)
+
+
+@router.delete("/{profile_id}/mounts/{mount_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def remove_profile_mount(
+    profile_id: uuid.UUID,
+    mount_id: uuid.UUID,
+    user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+) -> None:
+    await get_owned_profile(profile_id, user_id, session)
+    mount = await session.get(ConfigMount, mount_id)
+    if mount is None or mount.profile_id != profile_id:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="mount not found")
+    await session.delete(mount)
+    await session.commit()

apps/api/src/api/dashboard.py

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

apps/api/src/api/git_repositories.py

@@ -0,0 +1,290 @@
+"""Git repository API endpoints."""
+
+import logging
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, Response, status
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from src.auth.dependencies import get_current_user, get_db_session, get_owned_project
+from src.models.project import Project
+from src.models.user import User
+from src.schemas.git_repository import (
+    BranchCreateRequest,
+    CheckoutRequest,
+    CommitRequest,
+    CommitResponse,
+    FetchResponse,
+    FileContentResponse,
+    FileListResponse,
+    FileUpdateRequest,
+    FileUpdateResponse,
+    GitRepositoryCreate,
+    GitRepositoryResponse,
+    MergeRequest,
+    MergeResponse,
+    PullResponse,
+    PushResponse,
+    StatusResponse,
+    URLParseRequest,
+    URLParseResponse,
+)
+from src.services.git import control as git_control
+from src.services.git import files as git_files
+from src.services.git.repository import create_repository, delete_repository, list_repositories
+from src.utils.git_url_parser import parse_git_url
+
+router = APIRouter(prefix="/projects", tags=["git-repositories"])
+logger = logging.getLogger(__name__)
+
+
+@router.get("/{project_id}/repositories", response_model=list[GitRepositoryResponse])
+async def list_repositories_endpoint(
+    project_id: uuid.UUID,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+):
+    return await list_repositories(session, project_id)
+
+
+@router.post("/{project_id}/repositories", response_model=GitRepositoryResponse, status_code=status.HTTP_201_CREATED)
+async def create_repository_endpoint(
+    project_id: uuid.UUID,
+    data: GitRepositoryCreate,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+):
+    return await create_repository(session, project_id, data, user)
+
+
+@router.delete("/{project_id}/repositories/{repo_id}", status_code=status.HTTP_204_NO_CONTENT)
+async def delete_repository_endpoint(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+):
+    await delete_repository(session, repo_id, project_id)
+    return Response(status_code=status.HTTP_204_NO_CONTENT)
+
+
+@router.post("/repositories/parse-url", response_model=URLParseResponse)
+async def parse_repository_url(data: URLParseRequest) -> URLParseResponse:
+    return URLParseResponse(**parse_git_url(data.url))
+
+
+# History
+
+@router.get("/{project_id}/repositories/{repo_id}/history")
+async def get_repository_history(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    view: str = "graph",
+    branch: str | None = None,
+    limit: int = 100,
+    offset: int = 0,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    from src.utils.git_history import get_commit_history
+    from src.services.git.repository import get_repo_and_validate, ensure_repo_on_disk
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        return get_commit_history(repo.path, branch=branch, limit=limit, offset=offset)
+    except RuntimeError as e:
+        logger.warning("Git history failed for %s: %s", repo.path, str(e))
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"Git history unavailable: {str(e)}",
+        ) from e
+
+
+@router.get("/{project_id}/repositories/{repo_id}/commits/{commit_hash}")
+async def get_repository_commit(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    commit_hash: str,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    from src.utils.git_history import get_commit_detail
+    from src.services.git.repository import get_repo_and_validate, ensure_repo_on_disk
+    repo = await get_repo_and_validate(session, repo_id, project_id)
+    ensure_repo_on_disk(repo)
+    try:
+        return get_commit_detail(repo.path, commit_hash)
+    except RuntimeError as e:
+        logger.warning("Git commit detail failed for %s %s: %s", repo.path, commit_hash, str(e))
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail=f"Commit detail unavailable: {str(e)}",
+        ) from e
+
+
+# File browsing
+
+@router.get("/{project_id}/repositories/{repo_id}/files", response_model=FileListResponse)
+async def list_repository_files(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch: str = "main",
+    path: str = "",
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> FileListResponse:
+    return await git_files.list_files(session, project_id, repo_id, branch, path)
+
+
+@router.get("/{project_id}/repositories/{repo_id}/files/content", response_model=FileContentResponse)
+async def get_repository_file_content(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch: str,
+    path: str,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> FileContentResponse:
+    return await git_files.get_file(session, project_id, repo_id, branch, path)
+
+
+@router.post("/{project_id}/repositories/{repo_id}/files/content", response_model=FileUpdateResponse)
+async def update_repository_file(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: FileUpdateRequest,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> FileUpdateResponse:
+    return await git_files.update_file(session, project_id, repo_id, data, user)
+
+
+# Branches
+
+@router.get("/{project_id}/repositories/{repo_id}/branches")
+async def get_repository_branches(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    return await git_files.list_branches_with_validation(session, project_id, repo_id)
+
+
+@router.post("/{project_id}/repositories/{repo_id}/branches")
+async def create_repository_branch(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: BranchCreateRequest,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    return await git_control.create_branch_with_validation(session, project_id, repo_id, data)
+
+
+@router.delete("/{project_id}/repositories/{repo_id}/branches/{branch_name}")
+async def delete_repository_branch(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch_name: str,
+    force: bool = False,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    return await git_control.delete_branch_with_validation(session, project_id, repo_id, branch_name, force)
+
+
+@router.post("/{project_id}/repositories/{repo_id}/checkout")
+async def checkout_repository_branch(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: CheckoutRequest,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> dict:
+    return await git_control.checkout_branch_with_validation(session, project_id, repo_id, data)
+
+
+# Git control
+
+@router.get("/{project_id}/repositories/{repo_id}/status", response_model=StatusResponse)
+async def get_repository_status(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> StatusResponse:
+    return await git_control.get_status_with_validation(session, project_id, repo_id)
+
+
+@router.post("/{project_id}/repositories/{repo_id}/commit", response_model=CommitResponse)
+async def commit_repository_changes(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: CommitRequest,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> CommitResponse:
+    result = await git_control.commit_changes_with_validation(session, project_id, repo_id, data, user)
+    return CommitResponse(commit_hash=result["commit_hash"], message=result["message"])
+
+
+@router.post("/{project_id}/repositories/{repo_id}/fetch", response_model=FetchResponse)
+async def fetch_repository(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> FetchResponse:
+    return await git_control.fetch_with_validation(session, project_id, repo_id)
+
+
+@router.post("/{project_id}/repositories/{repo_id}/pull", response_model=PullResponse)
+async def pull_repository(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch: str | None = None,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> PullResponse:
+    return await git_control.pull_with_validation(session, project_id, repo_id, branch)
+
+
+@router.post("/{project_id}/repositories/{repo_id}/push", response_model=PushResponse)
+async def push_repository(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    branch: str | None = None,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> PushResponse:
+    return await git_control.push_with_validation(session, project_id, repo_id, branch)
+
+
+@router.post("/{project_id}/repositories/{repo_id}/merge", response_model=MergeResponse)
+async def merge_repository_branches(
+    project_id: uuid.UUID,
+    repo_id: uuid.UUID,
+    data: MergeRequest,
+    user: User = Depends(get_current_user),
+    project: Project = Depends(get_owned_project),
+    session: AsyncSession = Depends(get_db_session),
+) -> MergeResponse:
+    return await git_control.merge_with_validation(session, project_id, repo_id, data)

apps/api/src/api/health.py

@@ -4,11 +4,12 @@ import time
 from datetime import datetime, timezone
 from typing import Any
 
-from fastapi import APIRouter
+from fastapi import APIRouter, status
 from sqlalchemy import text
 
+from src.config import Settings
 from src.database import SessionLocal
-from src.schemas.system import (
+from src.schemas.health import (
     DatabaseHealth,
     DatabaseHealthResponse,
     DiskHealth,