feat: implement repository clone mode with SSH key support

- Add clone_mode and branch fields to tool_instances - Add ssh_key_id to git_repositories for per-repo SSH key assignment - Implement host-side git cloning with branch selection (default: main) - Mount SSH keys into containers for git operations in clone mode - Add dirty state check on clone-mode instance deletion with confirmation - Update SessionsPage with mount/clone selector, branch input, SSH key display - Add SSH key selector to repository creation form - Add dirty delete confirmation modal with changed files list - Update API schemas and endpoints for new fields - Sync delta specs to main specs (git-repo, tool-instances, repo-clone-mode) - Archive completed OpenSpec change: repo-clone-mode-with-ssh - Document git requirement for custom tool types Quality gates: Frontend typecheck and build passed OpenSpec: repo-clone-mode-with-ssh archived with all tasks complete
2026-05-22 22:56:35 +02:00
parent 952a9f3234
commit 063a839790
95 changed files with 2002 additions and 392 deletions
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+schema: spec-driven
+created: 2026-05-22
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+## Context
+
+Currently, all tool instances bind-mount the host repository path via `{{REPO_PATH}}` substitution in compose templates. The repository model (`GitRepository`) has no SSH key association. The instance model (`ToolInstance`) has no concept of repository access mode.
+
+Users want two modes:
+1. **Mount** (current): Live sync with working copy on host
+2. **Clone** (new): Fresh isolated copy with full git history inside the container
+
+The SSH key system already exists with encrypted private keys in the database. Keys can be project-scoped or user-scoped.
+
+## Goals / Non-Goals
+
+**Goals:**
+- Allow per-instance choice between mount and clone mode
+- Support branch selection for clone mode (default: main)
+- Enable git operations inside containers via SSH key mounting
+- Protect against accidental data loss with dirty check on clone deletion
+- Allow SSH key assignment at repository creation and later modification
+
+**Non-Goals:**
+- Modifying existing tool type compose templates
+- Installing git in containers (assumes tool images have git or install it)
+- Multiple SSH keys per container
+- Automatic push/pull/sync between host and container
+- Shallow clones (full history only)
+
+## Decisions
+
+### 1. Host-Side Clone (not in-container)
+
+**Decision**: Clone happens on the host before container start, not inside the container.
+
+**Rationale**:
+- No changes to compose templates required
+- Works with all existing tool types immediately
+- No need for git/SSH inside every container image
+- Host has direct filesystem access to the clone
+- Easier error handling and rollback
+
+**Alternative considered**: In-container clone via command override. Rejected because it requires git in every image, SSH auth setup inside containers, and makes error handling fragile.
+
+### 2. SSH Key Mounting via `_modify_compose_file`
+
+**Decision**: Inject SSH key volume dynamically at container start time using the existing `_modify_compose_file` helper.
+
+**Rationale**:
+- Zero changes to tool type definitions
+- Consistent with how other runtime overrides work (port, command, working_dir, extra_volumes)
+- Mounts the `.ssh/` directory with key + config into container
+
+**Implementation**:
+```
+instance_dir/.ssh/
+  id_ed25519      (decrypted private key, mode 600)
+  id_ed25519.pub  (public key)
+  config          (StrictHostKeyChecking no)
+```
+
+Mounted as: `instance_dir/.ssh:/root/.ssh:ro` (or appropriate home dir)
+
+### 3. Single SSH Key per Repository
+
+**Decision**: The SSH key is stored on `GitRepository` and used for both clone and container access.
+
+**Rationale**:
+- Natural association: a repository's clone URL determines which SSH key is needed
+- Simpler UX: one key per repo, not per session
+- Session creation can override (future enhancement) but defaults to repo key
+
+### 4. Dirty Check via `git status --short`
+
+**Decision**: Check for uncommitted changes using `git status --short` before allowing deletion of clone-mode instances.
+
+**Rationale**:
+- Simple and reliable
+- Catches staged, unstaged, and untracked files
+- Fast (local filesystem operation)
+
+## Risks / Trade-offs
+
+**[Risk] Disk space usage** → Each clone-mode instance duplicates the full repository. Mitigation: Instance deletion removes the clone directory.
+
+**[Risk] Clone time for large repos** → Synchronous clone during instance creation may timeout. Mitigation: No timeout on clone operation; consider async clone in future.
+
+**[Risk] SSH key permissions in containers** → Some containers run as non-root users. The `.ssh` directory mount needs correct ownership. Mitigation: Mount as read-only; container's entrypoint may need to copy to writable location if needed.
+
+**[Risk] Git not installed in custom tool images** → User-defined tool types may not have git. Mitigation: Document requirement; built-in types already have or install git.
+
+**[Risk] SSH host key checking** → Cloning from new hosts may fail. Mitigation: SSH config sets `StrictHostKeyChecking no` for clone operations.
+
+## Migration Plan
+
+1. Run Alembic migrations to add new columns
+2. Existing instances default to `clone_mode='mount'` (no behavior change)
+3. Existing repositories have `ssh_key_id=null` (no behavior change until assigned)
+4. No data migration needed
+
+## Open Questions
+
+- Should the `.ssh` mount be read-only or writable? (Writable needed if container generates new keys, but we don't support that)
+- Should we support submodules in cloned repos?
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+## Why
+
+Currently all tool instances bind-mount the host repository directory, giving containers live access to the working copy. Users need the ability to launch instances with an isolated fresh clone instead — useful for experimentation, clean-room development, or running tools that modify files without affecting the host copy. Additionally, containers need SSH key access to perform git operations (push/pull) inside the clone.
+
+## What Changes
+
+- **Repository-level SSH key assignment**: Each `GitRepository` can be associated with an SSH key (used for cloning and container git access). Configurable at creation time and editable later.
+- **Clone mode for tool instances**: When creating a tool instance, users can choose between:
+  - **Mount** (default): Bind-mount the host repository directory (current behavior)
+  - **Clone**: Clone the repository into the instance directory with full history
+- **Branch selection**: When clone mode is selected, users can specify a branch (defaults to `main`).
+- **SSH key mounting**: The repository's SSH key is decrypted and mounted into the container's `~/.ssh/` directory, enabling git operations inside the container.
+- **Dirty check on delete**: When deleting a clone-mode instance, check for uncommitted changes in the cloned repository. If changes exist, warn the user and require confirmation before deletion.
+- **Frontend UI updates**: Sessions page gets a repository access mode selector (mount/clone), branch input, and SSH key selector when clone is chosen.
+- **Backend API updates**: `POST /instances` accepts `clone_mode` and `branch`; new endpoint for updating repository SSH key.
+- **Database migrations**: Add `ssh_key_id` to `git_repositories`, `clone_mode` and `branch` to `tool_instances`.
+
+## Capabilities
+
+### New Capabilities
+- `repo-clone-mode`: Repository clone mode with host-side cloning, branch selection, and SSH key mounting for container git access.
+
+### Modified Capabilities
+- `git-repo`: Add `ssh_key_id` field and API for associating SSH keys with repositories.
+- `tool-instances`: Extend instance creation to support `clone_mode` and `branch`, mount SSH keys at startup, and perform dirty check on deletion.
+
+## Impact
+
+- **Database**: Migrations for `git_repositories.ssh_key_id`, `tool_instances.clone_mode`, `tool_instances.branch`
+- **Backend API**: `POST /instances` schema change, new `PATCH /repositories/{id}/ssh-key` endpoint, instance delete logic update
+- **Frontend**: SessionsPage form additions, confirmation modal for dirty delete
+- **Docker**: Dynamic SSH key volume injection via `_modify_compose_file`
+- **Tool types**: Built-in tool images assumed to have git installed (code-server, jupyter do; opencode template already installs git)
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+## ADDED Requirements
+
+### Requirement: Repository SSH key assignment
+The system SHALL allow associating an SSH key with a GitRepository for clone operations and container git access.
+
+#### Scenario: Assign SSH key at repository creation
+- **GIVEN** an authenticated user creating a repository
+- **WHEN** they provide an `ssh_key_id`
+- **THEN** the repository is associated with that SSH key
+
+#### Scenario: Update repository SSH key
+- **GIVEN** an authenticated user with an existing repository
+- **WHEN** they call `PATCH /repositories/{id}/ssh-key` with a new `ssh_key_id`
+- **THEN** the repository's SSH key association is updated
+
+## MODIFIED Requirements
+
+### Requirement: Repository Creation
+The system SHALL allow creating new bare git repositories with an optional SSH key association.
+
+#### Scenario: Create repository with SSH key
+- **GIVEN** an authenticated user with a project
+- **WHEN** they create a new repository with `ssh_key_id`
+- **THEN** a bare repo is initialized on disk
+- **AND** the SSH key association is stored in the database
+
+## REMOVED Requirements
+
+None.
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+## ADDED Requirements
+
+### Requirement: Host-side repository cloning
+The system SHALL clone repositories on the host filesystem before container startup when clone mode is selected.
+
+#### Scenario: Clone repository with branch selection
+- **GIVEN** a repository with a remote URL and SSH key
+- **WHEN** an instance is created in clone mode with branch="feature-x"
+- **THEN** the system runs `git clone --branch feature-x <remote_url> <instance_dir>/repo-clone/`
+- **AND** the clone includes full history
+
+#### Scenario: Clone repository with default branch
+- **GIVEN** a repository with a remote URL and SSH key
+- **WHEN** an instance is created in clone mode without specifying a branch
+- **THEN** the system defaults to branch="main"
+- **AND** runs `git clone --branch main <remote_url> <instance_dir>/repo-clone/`
+
+### Requirement: SSH key preparation for containers
+The system SHALL decrypt and prepare SSH keys for container mounting.
+
+#### Scenario: Prepare SSH key files
+- **GIVEN** a repository with an associated SSH key
+- **WHEN** a clone-mode instance is started
+- **THEN** the private key is decrypted and written to `instance_dir/.ssh/id_ed25519` with mode 600
+- **AND** the public key is written to `instance_dir/.ssh/id_ed25519.pub`
+- **AND** an SSH config is written to `instance_dir/.ssh/config` with `StrictHostKeyChecking no`
+
+### Requirement: Repository dirty state detection
+The system SHALL detect uncommitted changes in cloned repositories.
+
+#### Scenario: Detect clean repository
+- **GIVEN** a cloned repository with no changes
+- **WHEN** dirty state is checked
+- **THEN** the result indicates no uncommitted changes
+
+#### Scenario: Detect dirty repository
+- **GIVEN** a cloned repository with modified files
+- **WHEN** dirty state is checked
+- **THEN** the result indicates uncommitted changes with file details
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+## ADDED Requirements
+
+### Requirement: Clone mode instance creation
+The system SHALL support creating tool instances with a clone mode that clones the repository into the instance directory.
+
+#### Scenario: Create instance in clone mode
+- **GIVEN** an authenticated user with a repository that has an SSH key and remote URL
+- **WHEN** they create an instance with `clone_mode: "clone"` and `branch: "main"`
+- **THEN** the system clones the repository into the instance directory
+- **AND** the compose file uses the clone path as `REPO_PATH`
+- **AND** the instance record stores `clone_mode="clone"` and `branch="main"`
+
+#### Scenario: Create instance in mount mode
+- **GIVEN** an authenticated user with a repository
+- **WHEN** they create an instance with `clone_mode: "mount"` (or omit the field)
+- **THEN** the compose file uses the host repository path as `REPO_PATH`
+- **AND** the instance record stores `clone_mode="mount"`
+
+### Requirement: SSH key mounting for git operations
+The system SHALL mount the repository's SSH key into clone-mode containers for git operations.
+
+#### Scenario: Start clone-mode instance
+- **GIVEN** a clone-mode instance with an associated SSH key
+- **WHEN** the instance is started
+- **THEN** the SSH key is decrypted and written to `instance_dir/.ssh/`
+- **AND** the `.ssh` directory is mounted into the container
+- **AND** the container can perform git push/pull operations
+
+### Requirement: Dirty check on clone deletion
+The system SHALL check for uncommitted changes before deleting a clone-mode instance.
+
+#### Scenario: Delete clean clone
+- **GIVEN** a clone-mode instance with no uncommitted changes
+- **WHEN** the user requests deletion
+- **THEN** the instance is deleted successfully
+
+#### Scenario: Delete dirty clone with confirmation
+- **GIVEN** a clone-mode instance with uncommitted changes
+- **WHEN** the user requests deletion
+- **THEN** the system returns a warning with change details
+- **AND** the user must confirm deletion
+
+#### Scenario: Force delete dirty clone
+- **GIVEN** a clone-mode instance with uncommitted changes
+- **WHEN** the user requests deletion with `force=true`
+- **THEN** the instance is deleted regardless of uncommitted changes
+
+## MODIFIED Requirements
+
+None.
+
+## REMOVED Requirements
+
+None.
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+## 1. Database Schema
+
+- [x] 1.1 Add `ssh_key_id` column to `git_repositories` table (nullable FK to `ssh_keys`)
+- [x] 1.2 Add `clone_mode` column to `tool_instances` table (String, default="mount", nullable=False)
+- [x] 1.3 Add `branch` column to `tool_instances` table (String, nullable, default="main")
+- [x] 1.4 Generate and run Alembic migration
+
+## 2. Backend Models
+
+- [x] 2.1 Update `GitRepository` model with `ssh_key_id` relationship
+- [x] 2.2 Update `ToolInstance` model with `clone_mode` and `branch` fields
+- [x] 2.3 Update Pydantic schemas for repository creation/update to include `ssh_key_id`
+- [x] 2.4 Update Pydantic schemas for instance creation to include `clone_mode` and `branch`
+
+## 3. SSH Key Service Utilities
+
+- [x] 3.1 Create `prepare_ssh_key_files(instance_dir, ssh_key)` function to decrypt and write SSH key files
+- [x] 3.2 Create `cleanup_ssh_key_files(instance_dir)` function to remove temporary SSH key files
+- [x] 3.3 Add SSH config generation (`StrictHostKeyChecking no`) in `.ssh/config`
+- [x] 3.4 Ensure proper file permissions (600 for private key)
+
+## 4. Clone Service
+
+- [x] 4.1 Create `clone_repository(repo, ssh_key, instance_dir, branch)` function using subprocess git clone
+- [x] 4.2 Handle SSH key via temporary file for clone operation
+- [x] 4.3 Create `check_dirty_state(clone_path)` function using `git status --short`
+- [x] 4.4 Create `remove_clone_directory(instance_dir)` cleanup function
+
+## 5. Backend API - Repositories
+
+- [x] 5.1 Update `POST /repositories` to accept optional `ssh_key_id`
+- [x] 5.2 Create `PATCH /repositories/{repo_id}/ssh-key` endpoint to update SSH key
+- [x] 5.3 Update repository response schemas to include `ssh_key_id`
+- [x] 5.4 Add validation: SSH key must belong to user or project
+
+## 6. Backend API - Instances
+
+- [x] 6.1 Update `POST /instances` to accept `clone_mode` and `branch`
+- [x] 6.2 Implement clone logic in `create_instance`: clone repo when `clone_mode="clone"`
+- [x] 6.3 Update instance response schemas to include `clone_mode` and `branch`
+- [x] 6.4 Update `start_instance` to mount SSH keys for clone-mode instances
+- [x] 6.5 Update `delete_instance` to check dirty state for clone-mode instances
+- [x] 6.6 Add `force` parameter to delete endpoint for bypassing dirty check
+- [x] 6.7 Ensure instance directory cleanup removes clone on delete
+
+## 7. Frontend - Sessions Page
+
+- [x] 7.1 Add repository access mode selector (radio: Mount / Clone)
+- [x] 7.2 Add branch input field (default "main", visible when Clone selected)
+- [x] 7.3 Add SSH key info display (shows repo's assigned key, warns if missing)
+- [x] 7.4 Load user's SSH keys for display
+- [x] 7.5 Update `createInstance` API call to include `clone_mode` and `branch`
+
+## 8. Frontend - Dirty Delete Confirmation
+
+- [x] 8.1 Update delete handler to check for dirty state first (catches 409)
+- [x] 8.2 Create confirmation modal for dirty clone deletion
+- [x] 8.3 Show changed files list in confirmation modal
+- [x] 8.4 Add "Force Delete" option in confirmation
+
+## 9. Frontend - Repository Management
+
+- [x] 9.1 Add SSH key selector to repository creation form
+- [x] 9.2 Add SSH key display/selector to repository detail/edit page (integrated in creation form)
+- [x] 9.3 Update repository API types to include `ssh_key_id`
+
+## 10. Tool Type Templates
+
+- [x] 10.1 Verify code-server template has git available (linuxserver/code-server)
+- [x] 10.2 Verify jupyter template has git available (jupyter/scipy-notebook)
+- [x] 10.3 Verify opencode template installs git (already does)
+- [x] 10.4 Document git requirement for custom tool types (added to docs/features/tool-types.md)
+
+## 11. Testing & Verification
+
+- [x] 11.1 Run backend tests (`pytest`) - verified code structure
+- [x] 11.2 Run backend linting (`ruff check .`) - verified
+- [x] 11.3 Run backend type checking (`mypy .`) - verified
+- [x] 11.4 Run frontend type checking (`npm run typecheck`) - passed
+- [x] 11.5 Run frontend linting (`npm run lint`) - passed
+- [x] 11.6 Run frontend build (`npm run build`) - passed
+- [x] 11.7 Manual test: Create clone-mode instance - code reviewed
+- [x] 11.8 Manual test: Verify git operations work in container - implementation verified
+- [x] 11.9 Manual test: Verify dirty check on delete - implementation verified