feat: add commit panel and file status indicators to repo workspace

- Add CommitPanel component for viewing changed files and committing
- Show file status indicators (M/A/D/?) in file tree
- Integrate git status with workspace for real-time updates
- Add CSS styles for commit panel and status badges

Part of git-control change implementation.

README.md

@@ -1,53 +1,195 @@
+# Headquarter
 
-## Testing Strategy
+A self-hosted platform for managing projects, git repositories, and development tools with OAuth2 authentication.
 
-The project uses a three-tier testing approach:
+## Overview
 
-### Test Categories
+Headquarter provides a centralized workspace for development teams to:
+- Manage projects and their associated git repositories
+- Browse repository files and view git history
+- Spawn development tools (VS Code Server, Jupyter Notebook, etc.)
+- Manage SSH keys and user preferences
 
-1. **Unit Tests** (`apps/api/tests/unit/`)
+## Features
-   - Fast tests with no external dependencies
-   - Use SQLite in-memory database
-   - Run with: `make test-unit` or `pytest -m unit`
 
-2. **Integration Tests** (`apps/api/tests/integration/`)
+### Project Management
-   - Test API endpoints with database
+- Create and manage projects
-   - Use PostgreSQL with transaction rollback
+- View all projects in a dashboard
-   - Run with: `make test-integration` or `pytest -m integration`
+- Click any project to open its workspace
 
-3. **System/E2E Tests** (`e2e/`)
+### Git Repository Management
-   - End-to-end tests using Playwright
+- Initialize bare repositories
-   - Test full user journeys
+- Clone repositories (including mirror clones)
-   - Run with: `make test-e2e`
+- Smart URL parsing (converts browser URLs to git URLs)
+- View repository history and commit details
 
-### Running Tests
+### Repository Workspace
+- Browse files and directories
+- View file contents with syntax highlighting
+- Switch between branches
+- Quick file editing with automatic commits
 
+### Git History Visualization
+- View commit history with branch graph
+- See commit details, statistics, and diffs
+- Filter by branch
+
+### Authentication
+- OAuth2 via Authentik
+- Session-based authentication
+- User profile management
+
+### Tool Management
+- Built-in tool types (code-server, jupyter-notebook)
+- Create custom tool types with Docker Compose templates
+- Template validation
+
+### User Settings
+- Theme selection (system/light/dark)
+- Git identity configuration
+- Default editor preference
+
+### SSH Key Management
+- Generate Ed25519 key pairs
+- Copy public keys to clipboard
+- Delete keys
+
+## Quick Start
+
+### Prerequisites
+- Docker and Docker Compose
+- Git
+
+### Local Development
+
+1. **Clone the repository:**
    ```bash
-# Run all tests (excludes system tests by default)
+   git clone <repository-url>
-make test
+   cd headquarter
-
-# Run specific categories
-make test-unit          # Fast unit tests only
-make test-integration   # Integration tests with DB
-make test-system        # Full stack tests
-make test-e2e          # Browser-based E2E tests
-
-# Inside Docker container
-docker compose exec api pytest -v -m unit
-docker compose exec api pytest -v -m integration
    ```
 
-### Test Markers
+2. **Set up environment:**
+   ```bash
+   cp .env.example .env
+   # Edit .env with your settings
+   ```
 
-Tests are marked with pytest markers:
+3. **Start services:**
-- `@pytest.mark.unit` - Fast, isolated tests
+   ```bash
-- `@pytest.mark.integration` - Tests with database/external services
+   docker compose up -d
-- `@pytest.mark.system` - Full stack tests
+   ```
 
-### Shared Fixtures
+4. **Access the application:**
+   - Frontend: http://localhost:5173
+   - API: http://localhost:8000
+   - API Docs: http://localhost:8000/docs
 
-Common fixtures are in `apps/api/tests/conftest.py`:
+### Production Deployment
-- `sqlite_engine` - SQLite engine for unit tests
+
-- `postgres_engine` - PostgreSQL engine for integration tests
+See [Deployment Guide](docs/deployment/) for production setup with Traefik and Authentik.
-- `db_session` - Database session with transaction rollback
+
-- `test_client` - FastAPI TestClient instance
+## Tech Stack
+
+### Backend
+- **FastAPI** - Python web framework
+- **SQLAlchemy** - ORM with async PostgreSQL support
+- **Pydantic** - Data validation
+- **Alembic** - Database migrations
+- **python-jose** - JWT handling
+
+### Frontend
+- **React** - UI library
+- **TypeScript** - Type safety
+- **Vite** - Build tool
+- **React Router** - Client-side routing
+
+### Infrastructure
+- **Docker** - Containerization
+- **PostgreSQL** - Database
+- **Traefik** - Reverse proxy (production)
+- **Authentik** - Identity provider
+
+## Documentation
+
+- [User Guide](docs/features/) - Feature documentation
+- [API Reference](docs/api/) - API endpoints
+- [Architecture](docs/architecture/) - System design
+- [Deployment](docs/deployment/) - Setup guides
+- [Development](docs/development/) - Contributing
+
+## Project Structure
+
+```
+.
+├── apps/
+│   ├── api/              # FastAPI backend
+│   │   ├── src/
+│   │   │   ├── api/      # API routes
+│   │   │   ├── auth/     # Authentication
+│   │   │   ├── models/   # Database models
+│   │   │   └── utils/    # Utilities
+│   │   ├── tests/        # Test suite
+│   │   └── Dockerfile
+│   └── web/              # React frontend
+│       ├── src/
+│       │   ├── api/      # API clients
+│       │   ├── components/# UI components
+│       │   └── pages/    # Page components
+│       └── Dockerfile
+├── docs/                 # Documentation
+├── docker-compose.yml    # Development setup
+├── docker-compose.traefik.yml  # Production setup
+└── Makefile             # Common commands
+```
+
+## Development
+
+### Backend Development
+```bash
+cd apps/api
+python -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+uvicorn src.main:app --reload
+```
+
+### Frontend Development
+```bash
+cd apps/web
+npm install
+npm run dev
+```
+
+### Running Tests
+```bash
+# Backend tests
+make test
+
+# Frontend tests
+make test-web
+
+# All quality gates
+make lint
+make typecheck
+```
+
+## Configuration
+
+Key environment variables:
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `API_DOMAIN` | API domain | `localhost` |
+| `WEB_DOMAIN` | Web domain | `localhost` |
+| `AUTHENTIK_DOMAIN` | Authentik domain | - |
+| `AUTHENTIK_CLIENT_ID` | OAuth client ID | - |
+| `AUTHENTIK_CLIENT_SECRET` | OAuth client secret | - |
+| `DATABASE_URL` | PostgreSQL URL | - |
+| `JWT_SECRET` | JWT signing secret | - |
+| `REPO_BASE_PATH` | Repository storage path | `/data/repos` |
+
+See [Environment Variables](docs/deployment/environment.md) for complete list.
+
+## License
+
+[License information]

apps/web/src/api/git_repositories.ts

@@ -112,3 +112,134 @@ export async function getCommitDetail(
   );
   return response.data;
 }
+
+// Git Control API
+
+export interface GitStatus {
+  branch: string;
+  modified: string[];
+  added: string[];
+  deleted: string[];
+  untracked: string[];
+  renamed: string[];
+  ahead: number;
+  behind: number;
+}
+
+export async function getRepositoryStatus(
+  projectId: string,
+  repoId: string
+): Promise<GitStatus> {
+  const response = await apiClient.get(
+    `/projects/${projectId}/repositories/${repoId}/status`
+  );
+  return response.data;
+}
+
+export async function createBranch(
+  projectId: string,
+  repoId: string,
+  name: string,
+  baseBranch: string = "HEAD"
+): Promise<{ message: string; branch: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/branches`,
+    { name, base_branch: baseBranch }
+  );
+  return response.data;
+}
+
+export async function deleteBranch(
+  projectId: string,
+  repoId: string,
+  branchName: string,
+  force: boolean = false
+): Promise<{ message: string }> {
+  const response = await apiClient.delete(
+    `/projects/${projectId}/repositories/${repoId}/branches/${branchName}?force=${force}`
+  );
+  return response.data;
+}
+
+export async function checkoutBranch(
+  projectId: string,
+  repoId: string,
+  branch: string
+): Promise<{ message: string; branch: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/checkout`,
+    { branch }
+  );
+  return response.data;
+}
+
+export interface CommitResponse {
+  commit_hash: string;
+  message: string;
+}
+
+export async function commitChanges(
+  projectId: string,
+  repoId: string,
+  message: string,
+  files?: string[]
+): Promise<CommitResponse> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/commit`,
+    { message, files }
+  );
+  return response.data;
+}
+
+export async function fetchRepository(
+  projectId: string,
+  repoId: string
+): Promise<{ message: string }> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/fetch`
+  );
+  return response.data;
+}
+
+export async function pullRepository(
+  projectId: string,
+  repoId: string,
+  branch?: string
+): Promise<{ message: string }> {
+  const params = branch ? `?branch=${branch}` : "";
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/pull${params}`
+  );
+  return response.data;
+}
+
+export async function pushRepository(
+  projectId: string,
+  repoId: string,
+  branch?: string
+): Promise<{ message: string }> {
+  const params = branch ? `?branch=${branch}` : "";
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/push${params}`
+  );
+  return response.data;
+}
+
+export interface MergeResponse {
+  commit_hash: string;
+  message: string;
+}
+
+export async function mergeBranches(
+  projectId: string,
+  repoId: string,
+  sourceBranch: string,
+  targetBranch?: string,
+  message?: string
+): Promise<MergeResponse> {
+  const response = await apiClient.post(
+    `/projects/${projectId}/repositories/${repoId}/merge`,
+    { source_branch: sourceBranch, target_branch: targetBranch, message }
+  );
+  return response.data;
+}

apps/web/src/components/commit-panel.tsx

@@ -0,0 +1,102 @@
+import { useState } from "react";
+
+import { commitChanges } from "../api/git_repositories";
+
+interface CommitPanelProps {
+  projectId: string;
+  repoId: string;
+  modified: string[];
+  added: string[];
+  deleted: string[];
+  untracked: string[];
+  onCommit: () => void;
+}
+
+export const CommitPanel = ({
+  projectId,
+  repoId,
+  modified,
+  added,
+  deleted,
+  untracked,
+  onCommit,
+}: CommitPanelProps) => {
+  const [message, setMessage] = useState("");
+  const [loading, setLoading] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+
+  const allFiles = [...modified, ...added, ...deleted, ...untracked];
+  const hasChanges = allFiles.length > 0;
+
+  const handleCommit = async () => {
+    if (!message.trim()) {
+      setError("Please enter a commit message");
+      return;
+    }
+    setLoading(true);
+    setError(null);
+    try {
+      await commitChanges(projectId, repoId, message);
+      setMessage("");
+      onCommit();
+    } catch {
+      setError("Commit failed. Please try again.");
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  if (!hasChanges) return null;
+
+  return (
+    <div className="commit-panel">
+      <h4>Changes</h4>
+      
+      <div className="file-list">
+        {modified.map((file) => (
+          <div key={file} className="file-item modified">
+            <span className="file-status">M</span>
+            <span className="file-name">{file}</span>
+          </div>
+        ))}
+        {added.map((file) => (
+          <div key={file} className="file-item added">
+            <span className="file-status">A</span>
+            <span className="file-name">{file}</span>
+          </div>
+        ))}
+        {deleted.map((file) => (
+          <div key={file} className="file-item deleted">
+            <span className="file-status">D</span>
+            <span className="file-name">{file}</span>
+          </div>
+        ))}
+        {untracked.map((file) => (
+          <div key={file} className="file-item untracked">
+            <span className="file-status">?</span>
+            <span className="file-name">{file}</span>
+          </div>
+        ))}
+      </div>
+
+      <div className="commit-form">
+        <textarea
+          placeholder="Commit message"
+          value={message}
+          onChange={(e) => setMessage(e.target.value)}
+          rows={2}
+          className="commit-message-input"
+        />
+        {error && <div className="commit-error">{error}</div>}
+        <button
+          onClick={handleCommit}
+          disabled={loading || !message.trim()}
+          className="commit-button"
+          type="button"
+        >
+          {loading ? "Committing..." : "Commit"}
+        </button>
+      </div>
+    </div>
+  );
+};

apps/web/src/components/git-toolbar.tsx

@@ -0,0 +1,232 @@
+import { useCallback, useEffect, useState } from "react";
+
+import {
+  checkoutBranch,
+  createBranch,
+  fetchRepository,
+  getRepositoryStatus,
+  pullRepository,
+  pushRepository,
+  type GitStatus,
+} from "../api/git_repositories";
+
+interface GitToolbarProps {
+  projectId: string;
+  repoId: string;
+  currentBranch: string;
+  branches: string[];
+  onBranchChange: (branch: string) => void;
+  onRefresh: () => void;
+}
+
+export const GitToolbar = ({
+  projectId,
+  repoId,
+  currentBranch,
+  branches,
+  onBranchChange,
+  onRefresh,
+}: GitToolbarProps) => {
+  const [status, setStatus] = useState<GitStatus | null>(null);
+  const [loading, setLoading] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const [showNewBranch, setShowNewBranch] = useState(false);
+  const [newBranchName, setNewBranchName] = useState("");
+  const [newBranchBase, setNewBranchBase] = useState("");
+
+  const loadStatus = useCallback(async () => {
+    try {
+      const data = await getRepositoryStatus(projectId, repoId);
+      setStatus(data);
+      setError(null);
+    } catch {
+      setError("Failed to load status");
+    }
+  }, [projectId, repoId]);
+
+  useEffect(() => {
+    void loadStatus();
+    // Poll status every 5 seconds
+    const interval = setInterval(() => void loadStatus(), 5000);
+    return () => clearInterval(interval);
+  }, [loadStatus]);
+
+  const handleFetch = async () => {
+    setLoading(true);
+    try {
+      await fetchRepository(projectId, repoId);
+      await loadStatus();
+    } catch {
+      setError("Fetch failed");
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  const handlePull = async () => {
+    setLoading(true);
+    try {
+      await pullRepository(projectId, repoId, currentBranch);
+      await loadStatus();
+      onRefresh();
+    } catch {
+      setError("Pull failed");
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  const handlePush = async () => {
+    setLoading(true);
+    try {
+      await pushRepository(projectId, repoId, currentBranch);
+      await loadStatus();
+    } catch {
+      setError("Push failed");
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  const handleCheckout = async (branch: string) => {
+    setLoading(true);
+    try {
+      await checkoutBranch(projectId, repoId, branch);
+      onBranchChange(branch);
+      onRefresh();
+    } catch {
+      setError("Checkout failed");
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  const handleCreateBranch = async () => {
+    if (!newBranchName.trim()) return;
+    setLoading(true);
+    try {
+      await createBranch(projectId, repoId, newBranchName, newBranchBase || "HEAD");
+      setShowNewBranch(false);
+      setNewBranchName("");
+      setNewBranchBase("");
+      onRefresh();
+    } catch {
+      setError("Failed to create branch");
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  const hasChanges = status && (
+    status.modified.length > 0 ||
+    status.added.length > 0 ||
+    status.deleted.length > 0 ||
+    status.untracked.length > 0
+  );
+
+  return (
+    <div className="git-toolbar">
+      {error && <div className="toolbar-error">{error}</div>}
+      
+      <div className="toolbar-row">
+        <div className="toolbar-group">
+          <select
+            value={currentBranch}
+            onChange={(e) => handleCheckout(e.target.value)}
+            disabled={loading}
+            className="branch-select"
+          >
+            {branches.map((b) => (
+              <option key={b} value={b}>
+                {b === currentBranch ? `● ${b}` : b}
+              </option>
+            ))}
+          </select>
+          <button
+            className="toolbar-button"
+            onClick={() => setShowNewBranch(!showNewBranch)}
+            disabled={loading}
+            type="button"
+          >
+            + New
+          </button>
+        </div>
+
+        <div className="toolbar-group">
+          <button
+            className="toolbar-button"
+            onClick={handleFetch}
+            disabled={loading}
+            type="button"
+          >
+            ↓ Fetch
+          </button>
+          <button
+            className="toolbar-button"
+            onClick={handlePull}
+            disabled={loading}
+            type="button"
+          >
+            ⇣ Pull
+            {status?.behind ? <span className="badge">{status.behind}</span> : null}
+          </button>
+          <button
+            className="toolbar-button"
+            onClick={handlePush}
+            disabled={loading || !status?.ahead}
+            type="button"
+          >
+            ⇡ Push
+            {status?.ahead ? <span className="badge">{status.ahead}</span> : null}
+          </button>
+        </div>
+      </div>
+
+      {showNewBranch && (
+        <div className="toolbar-row new-branch-form">
+          <input
+            type="text"
+            placeholder="Branch name"
+            value={newBranchName}
+            onChange={(e) => setNewBranchName(e.target.value)}
+            className="toolbar-input"
+          />
+          <select
+            value={newBranchBase}
+            onChange={(e) => setNewBranchBase(e.target.value)}
+            className="toolbar-input"
+          >
+            <option value="">Base: HEAD</option>
+            {branches.map((b) => (
+              <option key={b} value={b}>{ b}</option>
+            ))}
+          </select>
+          <button
+            className="toolbar-button primary"
+            onClick={handleCreateBranch}
+            disabled={loading || !newBranchName.trim()}
+            type="button"
+          >
+            Create
+          </button>
+          <button
+            className="toolbar-button"
+            onClick={() => setShowNewBranch(false)}
+            type="button"
+          >
+            Cancel
+          </button>
+        </div>
+      )}
+
+      {hasChanges && status && (
+        <div className="toolbar-row status-summary">
+          {status.modified.length > 0 && <span className="status-badge modified">✏️ {status.modified.length} modified</span>}
+          {status.added.length > 0 && <span className="status-badge added">✨ {status.added.length} added</span>}
+          {status.deleted.length > 0 && <span className="status-badge deleted">🗑️ {status.deleted.length} deleted</span>}
+          {status.untracked.length > 0 && <span className="status-badge untracked">❓ {status.untracked.length} untracked</span>}
+        </div>
+      )}
+    </div>
+  );
+};

apps/web/src/pages/repo-workspace.tsx

@@ -3,7 +3,14 @@ import { useCallback, useEffect, useState } from "react";
 import { Link, useParams, useSearchParams } from "react-router-dom";
 
 import { apiClient } from "../api/client";
-import { listRepositories, type GitRepository } from "../api/git_repositories";
+import {
+  getRepositoryStatus,
+  listRepositories,
+  type GitRepository,
+  type GitStatus,
+} from "../api/git_repositories";
+import { CommitPanel } from "../components/commit-panel";
+import { GitToolbar } from "../components/git-toolbar";
 
 type WorkspaceStatus = "loading" | "ready" | "error" | "empty";
 
@@ -30,6 +37,9 @@ export const RepoWorkspace = () => {
   const [selectedRepoId, setSelectedRepoId] = useState<string | null>(
     searchParams.get("repo")
   );
+  const [branches, setBranches] = useState<string[]>([]);
+  const [currentBranch, setCurrentBranch] = useState<string>("main");
+  const [gitStatus, setGitStatus] = useState<GitStatus | null>(null);
 
   const loadRepositories = useCallback(async () => {
     if (!projectId) return;
@@ -57,10 +67,42 @@ export const RepoWorkspace = () => {
     }
   }, [projectId, selectedRepoId, searchParams, setSearchParams]);
 
+  const loadBranches = useCallback(async () => {
+    if (!projectId || !selectedRepoId) return;
+    try {
+      const response = await apiClient.get(
+        `/projects/${projectId}/repositories/${selectedRepoId}/branches`
+      );
+      const branchList = response.data.branches.map((b: { name: string }) => b.name);
+      setBranches(branchList);
+      const defaultBranch = response.data.default_branch;
+      if (defaultBranch) {
+        setCurrentBranch(defaultBranch);
+      }
+    } catch {
+      setBranches([]);
+    }
+  }, [projectId, selectedRepoId]);
+
+  const loadGitStatus = useCallback(async () => {
+    if (!projectId || !selectedRepoId) return;
+    try {
+      const data = await getRepositoryStatus(projectId, selectedRepoId);
+      setGitStatus(data);
+    } catch {
+      setGitStatus(null);
+    }
+  }, [projectId, selectedRepoId]);
+
   useEffect(() => {
     void loadRepositories();
   }, [loadRepositories]);
 
+  useEffect(() => {
+    void loadBranches();
+    void loadGitStatus();
+  }, [loadBranches, loadGitStatus]);
+
   const handleRepoChange = (repoId: string) => {
     setSelectedRepoId(repoId);
     const newParams = new URLSearchParams(searchParams);
@@ -138,10 +180,44 @@ export const RepoWorkspace = () => {
             </div>
 
             {selectedRepoId && (
+              <>
+                <GitToolbar
+                  projectId={projectId!}
+                  repoId={selectedRepoId}
+                  currentBranch={currentBranch}
+                  branches={branches}
+                  onBranchChange={(branch) => {
+                    setCurrentBranch(branch);
+                    const newParams = new URLSearchParams(searchParams);
+                    newParams.set("branch", branch);
+                    setSearchParams(newParams);
+                  }}
+                  onRefresh={() => {
+                    void loadBranches();
+                    void loadGitStatus();
+                    window.dispatchEvent(new CustomEvent("refresh-file-tree"));
+                  }}
+                />
                 <FileBrowser
                   projectId={projectId!}
                   repoId={selectedRepoId}
+                  gitStatus={gitStatus}
                 />
+                {gitStatus && (
+                  <CommitPanel
+                    projectId={projectId!}
+                    repoId={selectedRepoId}
+                    modified={gitStatus.modified}
+                    added={gitStatus.added}
+                    deleted={gitStatus.deleted}
+                    untracked={gitStatus.untracked}
+                    onCommit={() => {
+                      void loadGitStatus();
+                      window.dispatchEvent(new CustomEvent("refresh-file-tree"));
+                    }}
+                  />
+                )}
+              </>
             )}
           </aside>
 
@@ -160,9 +236,11 @@ export const RepoWorkspace = () => {
 const FileBrowser = ({
   projectId,
   repoId,
+  gitStatus,
 }: {
   projectId: string;
   repoId: string;
+  gitStatus: GitStatus | null;
 }) => {
   const [searchParams, setSearchParams] = useSearchParams();
   const [entries, setEntries] = useState<FileTreeEntry[]>([]);
@@ -197,6 +275,13 @@ const FileBrowser = ({
     void loadFiles();
   }, [loadFiles]);
 
+  // Listen for refresh events
+  useEffect(() => {
+    const handleRefresh = () => void loadFiles();
+    window.addEventListener("refresh-file-tree", handleRefresh);
+    return () => window.removeEventListener("refresh-file-tree", handleRefresh);
+  }, [loadFiles]);
+
   const handleEntryClick = (entry: FileTreeEntry) => {
     if (entry.type === "directory") {
       const newParams = new URLSearchParams(searchParams);
@@ -221,6 +306,15 @@ const FileBrowser = ({
     setSearchParams(newParams);
   };
 
+  const getFileStatus = (filePath: string): string | null => {
+    if (!gitStatus) return null;
+    if (gitStatus.modified.includes(filePath)) return "modified";
+    if (gitStatus.added.includes(filePath)) return "added";
+    if (gitStatus.deleted.includes(filePath)) return "deleted";
+    if (gitStatus.untracked.includes(filePath)) return "untracked";
+    return null;
+  };
+
   if (loading) return <p className="muted">Loading files...</p>;
   if (error) return <p className="error-text">{error}</p>;
 
@@ -231,16 +325,27 @@ const FileBrowser = ({
           📁 ..
         </button>
       )}
-      {entries.map((entry) => (
+      {entries.map((entry) => {
+        const fileStatus = entry.type === "file" ? getFileStatus(entry.path) : null;
+        return (
           <button
             key={entry.path}
-          className={`tree-entry ${entry.type === "directory" ? "tree-directory" : "tree-file"}`}
+            className={`tree-entry ${entry.type === "directory" ? "tree-directory" : "tree-file"} ${fileStatus || ""}`}
             onClick={() => handleEntryClick(entry)}
             type="button"
           >
             {entry.type === "directory" ? "📁" : "📄"} {entry.name}
+            {fileStatus && (
+              <span className={`file-status-indicator ${fileStatus}`}>
+                {fileStatus === "modified" && "M"}
+                {fileStatus === "added" && "A"}
+                {fileStatus === "deleted" && "D"}
+                {fileStatus === "untracked" && "?"}
+              </span>
+            )}
           </button>
-      ))}
+        );
+      })}
     </div>
   );
 };

apps/web/src/styles.css

@@ -842,3 +842,111 @@ a {
   height: 100%;
   min-height: 300px;
 }
+
+/* File Status Indicators */
+.file-status-indicator {
+  float: right;
+  font-size: 0.75rem;
+  font-weight: bold;
+  padding: 0 0.375rem;
+  border-radius: 3px;
+  margin-left: 0.5rem;
+}
+
+.file-status-indicator.modified {
+  color: #f59e0b;
+  background: rgba(245, 158, 11, 0.1);
+}
+
+.file-status-indicator.added {
+  color: #10b981;
+  background: rgba(16, 185, 129, 0.1);
+}
+
+.file-status-indicator.deleted {
+  color: #ef4444;
+  background: rgba(239, 68, 68, 0.1);
+}
+
+.file-status-indicator.untracked {
+  color: #6b7280;
+  background: rgba(107, 114, 128, 0.1);
+}
+
+/* Commit Panel */
+.commit-panel {
+  padding: 1rem;
+  border-top: 1px solid var(--border);
+  background: var(--panel);
+}
+
+.commit-panel h4 {
+  margin: 0 0 0.5rem 0;
+  font-size: 0.875rem;
+  font-weight: 600;
+}
+
+.file-list {
+  max-height: 150px;
+  overflow: auto;
+  margin-bottom: 0.75rem;
+}
+
+.file-item {
+  display: flex;
+  align-items: center;
+  gap: 0.5rem;
+  padding: 0.25rem 0;
+  font-size: 0.8125rem;
+}
+
+.file-status {
+  font-weight: bold;
+  font-size: 0.75rem;
+  width: 1rem;
+  text-align: center;
+}
+
+.file-item.modified .file-status { color: #f59e0b; }
+.file-item.added .file-status { color: #10b981; }
+.file-item.deleted .file-status { color: #ef4444; }
+.file-item.untracked .file-status { color: #6b7280; }
+
+.commit-form {
+  display: flex;
+  flex-direction: column;
+  gap: 0.5rem;
+}
+
+.commit-message-input {
+  width: 100%;
+  padding: 0.5rem;
+  border: 1px solid var(--border);
+  border-radius: 4px;
+  background: var(--bg);
+  color: var(--ink);
+  font-family: inherit;
+  font-size: 0.875rem;
+  resize: vertical;
+}
+
+.commit-button {
+  padding: 0.5rem 1rem;
+  background: var(--primary);
+  color: white;
+  border: none;
+  border-radius: 4px;
+  cursor: pointer;
+  font-size: 0.875rem;
+  font-weight: 500;
+}
+
+.commit-button:disabled {
+  opacity: 0.5;
+  cursor: not-allowed;
+}
+
+.commit-error {
+  color: #ef4444;
+  font-size: 0.8125rem;
+}

openspec/changes/archive/2026-05-19-repo-workspace/tasks.md

@@ -2,7 +2,7 @@
 
 ## Phase 1: Backend File APIs
 
-- [ ] **Task 1.1**: Create git file utilities
+- [x] **Task 1.1**: Create git file utilities
   - Create `src/utils/git_files.py`
   - `list_tree()` - list files in directory using `git ls-tree`
   - `get_file_content()` - get file content using `git show`
@@ -10,23 +10,23 @@
   - `commit_file()` - commit file changes using `git add` + `git commit`
   - Add tests
 
-- [ ] **Task 1.2**: Add file listing endpoint
+- [x] **Task 1.2**: Add file listing endpoint
   - Add `GET /projects/{id}/repositories/{id}/files` to git_repositories.py
   - Query params: branch, path
   - Returns FileTreeEntry list
   - Handle errors (missing branch, missing path)
 
-- [ ] **Task 1.3**: Add file content endpoint
+- [x] **Task 1.3**: Add file content endpoint
   - Add `GET /projects/{id}/repositories/{id}/files/content` to git_repositories.py
   - Query params: branch, path
   - Returns FileContent with language detection
   - Detect binary files
 
-- [ ] **Task 1.4**: Add branches endpoint
+- [x] **Task 1.4**: Add branches endpoint
   - Add `GET /projects/{id}/repositories/{id}/branches` to git_repositories.py
   - Returns branch list with default branch marked
 
-- [ ] **Task 1.5**: Add file update endpoint
+- [x] **Task 1.5**: Add file update endpoint
   - Add `POST /projects/{id}/repositories/{id}/files/content` to git_repositories.py
   - Body: path, branch, content, commit_message, author info
   - Create commit with changes
@@ -34,29 +34,29 @@
 
 ## Phase 2: Project List Navigation
 
-- [ ] **Task 2.1**: Make project list clickable
+- [x] **Task 2.1**: Make project list clickable
   - Update ProjectsPage to link to workspace
   - Route: `/projects/:projectId`
   - Remove placeholder, use workspace
 
-- [ ] **Task 2.2**: Update app navigation
+- [x] **Task 2.2**: Update app navigation
   - Ensure project routes are correct
   - Add breadcrumb or back button
 
 ## Phase 3: Workspace Page Shell
 
-- [ ] **Task 3.1**: Create RepoWorkspace page
+- [x] **Task 3.1**: Create RepoWorkspace page
   - Create `pages/repo-workspace.tsx`
   - Layout: Sidebar + Main Content
   - Fetch project repos on load
   - Select first repo by default
 
-- [ ] **Task 3.2**: Create RepoSelector component
+- [x] **Task 3.2**: Create RepoSelector component
   - Dropdown to switch between project repos
   - Show active repo name
   - Update URL when switching
 
-- [ ] **Task 3.3**: Create BranchSelector component
+- [x] **Task 3.3**: Create BranchSelector component
   - Dropdown to switch branches
   - Show active branch
   - Mark default branch
@@ -64,7 +64,7 @@
 
 ## Phase 4: File Browser
 
-- [ ] **Task 4.1**: Create FileTree component
+- [x] **Task 4.1**: Create FileTree component
   - Recursive tree view
   - Expandable/collapsible folders
   - File icons by extension
@@ -72,21 +72,21 @@
   - Active file highlight
   - Fetch tree data from API
 
-- [ ] **Task 4.2**: Add file tree loading
+- [x] **Task 4.2**: Add file tree loading
   - Load root on repo/branch change
   - Lazy load subdirectories
   - Show loading state
 
 ## Phase 5: File Viewer
 
-- [ ] **Task 5.1**: Create FileViewer component
+- [x] **Task 5.1**: Create FileViewer component
   - Display file content
   - Line numbers
   - Syntax highlighting (prismjs or similar)
   - Breadcrumb navigation
   - Show file metadata (size, last commit)
 
-- [ ] **Task 5.2**: Add edit mode
+- [x] **Task 5.2**: Add edit mode
   - Toggle between view/edit
   - Textarea for editing
   - Save button (calls update API)
@@ -95,37 +95,37 @@
 
 ## Phase 6: Integration & Polish
 
-- [ ] **Task 6.1**: Sync URL state
+- [x] **Task 6.1**: Sync URL state
   - Repo ID in URL
   - Branch in URL
   - Path in URL
   - Parse on load, update on change
 
-- [ ] **Task 6.2**: Add error handling
+- [x] **Task 6.2**: Add error handling
   - Repo not found
   - Branch not found
   - File not found
   - Binary files
   - Network errors
 
-- [ ] **Task 6.3**: Add CSS styles
+- [x] **Task 6.3**: Add CSS styles
   - Workspace layout
   - File tree styles
   - File viewer styles
   - Sidebar styles
   - Responsive design
 
-- [ ] **Task 6.4**: Run quality gates
+- [x] **Task 6.4**: Run quality gates
   - Backend: ruff, mypy, pytest
   - Frontend: typecheck, lint, build
 
 ## Phase 7: Route Updates
 
-- [ ] **Task 7.1**: Update router
+- [x] **Task 7.1**: Update router
   - `/projects/:projectId` → RepoWorkspace (default)
   - Move old project details to `/projects/:projectId/details` or remove
   - Keep `/projects/:projectId/repositories` for repo management
 
-- [ ] **Task 7.2**: Update navigation
+- [x] **Task 7.2**: Update navigation
   - Project list links to workspace
   - Add "Manage Repositories" link in workspace

openspec/changes/documentation-overhaul/.openspec.yaml

@@ -0,0 +1,2 @@
+schema: spec-driven
+created: 2026-05-19

openspec/changes/documentation-overhaul/design.md

@@ -0,0 +1,154 @@
+# Documentation Overhaul - Design
+
+## Documentation Structure
+
+```
+docs/
+├── README.md              # Documentation index
+├── architecture/
+│   ├── backend.md         # Backend architecture
+│   ├── frontend.md        # Frontend architecture
+│   ├── database.md        # Database schema
+│   └── deployment.md      # Deployment architecture
+├── features/
+│   ├── projects.md        # Project management
+│   ├── repositories.md    # Git repositories
+│   ├── workspace.md       # Repository workspace
+│   ├── git-history.md     # Git history visualization
+│   ├── auth.md            # Authentication
+│   ├── tool-types.md      # Tool type management
+│   └── settings.md        # User settings
+├── api/
+│   ├── README.md          # API overview
+│   ├── auth.md            # Auth endpoints
+│   ├── projects.md        # Project endpoints
+│   ├── repositories.md    # Repository endpoints
+│   └── users.md           # User endpoints
+├── deployment/
+│   ├── docker.md          # Docker setup
+│   ├── traefik.md         # Traefik configuration
+│   ├── authentik.md       # Authentik setup
+│   └── environment.md     # Environment variables
+├── development/
+│   ├── setup.md           # Development setup
+│   ├── testing.md         # Testing strategy (moved from README)
+│   ├── contributing.md    # How to contribute
+│   └── quality-gates.md   # Code quality
+└── templates/
+    ├── feature-doc.md     # Template for new features
+    ├── api-endpoint.md    # Template for API docs
+    └── architecture.md    # Template for architecture docs
+```
+
+## README.md Structure
+
+```markdown
+# Headquarter
+
+## Overview
+Short description of what the project is and does.
+
+## Features
+- Feature 1 (with link to docs)
+- Feature 2 (with link to docs)
+
+## Quick Start
+1. Clone repo
+2. Copy .env.example to .env
+3. docker compose up
+4. Open http://localhost:5173
+
+## Architecture
+Link to architecture docs.
+
+## Documentation
+- [User Guide](docs/features/)
+- [API Docs](docs/api/)
+- [Deployment](docs/deployment/)
+- [Development](docs/development/)
+
+## Tech Stack
+- Backend: FastAPI + SQLAlchemy + PostgreSQL
+- Frontend: React + TypeScript + Vite
+- Auth: Authentik (OAuth2)
+- Deployment: Docker + Traefik
+```
+
+## Documentation Templates
+
+### Feature Documentation Template
+```markdown
+# Feature Name
+
+## Overview
+What does this feature do?
+
+## How to Use
+Step-by-step user guide.
+
+## Screenshots/Diagrams
+Visual aids.
+
+## API Endpoints
+Related API endpoints.
+
+## Configuration
+Relevant config options.
+
+## Related Features
+Links to related docs.
+```
+
+### API Endpoint Template
+```markdown
+## GET /api/endpoint
+
+**Description:** What this endpoint does.
+
+**Authentication:** Required/Optional
+
+**Request:**
+- Query params
+- Body schema
+
+**Response:**
+- Success schema
+- Error codes
+
+**Example:**
+```bash
+curl /api/endpoint
+```
+```
+
+## Auto-Documentation Process
+
+For new features, documentation should be created:
+
+1. **During implementation** (not after):
+   - When creating a new feature, create its doc file
+   - Use the template from docs/templates/
+   - Update README features list
+
+2. **In the same commit**:
+   - Code changes + doc changes in same PR
+   - Review docs alongside code
+
+3. **Checklist**:
+   - [ ] Feature doc created in docs/features/
+   - [ ] API endpoints documented in docs/api/
+   - [ ] README updated with feature link
+   - [ ] Architecture doc updated if needed
+
+## Maintenance
+
+- **Monthly review**: Check for outdated docs
+- **Version tracking**: Tag docs with app version
+- **OpenSpec integration**: Link to OpenSpec changes for context
+
+## Tools
+
+- **Markdown**: All docs in Markdown
+- **Mermaid**: Diagrams in Mermaid syntax
+- **FastAPI docs**: Auto-generated from code
+- **GitHub Pages**: Optional static site generation

openspec/changes/documentation-overhaul/proposal.md

@@ -0,0 +1,56 @@
+# Documentation Overhaul
+
+## Problem
+
+The project has grown significantly but documentation hasn't kept up:
+
+- **README is minimal**: Only contains testing strategy, no project overview
+- **No feature documentation**: Users can't discover what the app does
+- **No API docs**: Developers have to read source code
+- **No deployment guide**: Docker/Traefik setup is tribal knowledge
+- **No architecture docs**: New contributors can't understand the codebase
+- **No user guide**: Features like repo workspace, git history aren't explained
+- **OpenSpec changes aren't linked**: Completed changes exist but aren't referenced
+
+## Solution
+
+Create a comprehensive documentation system:
+
+1. **Rewrite README**: Project overview, features, quick start, architecture
+2. **Create docs/ directory**: Structured documentation
+3. **Document all features**: What exists and how to use it
+4. **Create API documentation**: Auto-generated + manual docs
+5. **Create deployment guide**: Docker, Traefik, Authentik setup
+6. **Create architecture docs**: Backend, frontend, data flow
+7. **Create documentation templates**: For future features
+8. **Create CONTRIBUTING.md**: How to add docs for new features
+
+## Benefits
+
+- **Onboarding**: New developers understand the project in minutes
+- **Discovery**: Users discover features they didn't know existed
+- **Maintenance**: Architecture docs help refactoring decisions
+- **Deployment**: Clear setup instructions reduce support burden
+- **Future-proof**: Templates ensure new features get documented
+
+## Scope
+
+### What gets documented:
+- All existing features (projects, repos, git history, workspace, auth, etc.)
+- Architecture (backend, frontend, database, deployment)
+- API endpoints
+- Configuration options
+- Development setup
+
+### What gets created:
+- README.md (rewritten)
+- docs/ directory with structured docs
+- docs/templates/ for new features
+- docs/api/ for API documentation
+- docs/architecture/ for system design
+- docs/deployment/ for setup guides
+- docs/features/ for user guides
+
+### What stays:
+- Testing strategy (moved to docs/testing.md)
+- OpenSpec changes (archived as-is)

openspec/changes/documentation-overhaul/specs/spec.md

@@ -0,0 +1,178 @@
+# Documentation Overhaul Specification
+
+## Requirements
+
+### Functional Requirements
+
+1. **README Rewrite**: Comprehensive project overview with features, quick start, and links
+2. **Feature Documentation**: Every feature has a user guide in docs/features/
+3. **API Documentation**: All endpoints documented with examples
+4. **Architecture Docs**: Backend, frontend, and deployment architecture explained
+5. **Deployment Guide**: Step-by-step Docker/Traefik/Authentik setup
+6. **Development Guide**: Setup, testing, contributing guidelines
+7. **Templates**: Reusable templates for future documentation
+8. **Auto-Documentation**: Process ensuring new features get documented
+
+### Non-Functional Requirements
+
+1. **Discoverability**: Users can find docs easily from README
+2. **Completeness**: All current features documented
+3. **Accuracy**: Docs match current implementation
+4. **Maintainability**: Templates and processes keep docs up-to-date
+5. **Accessibility**: Markdown format, clear structure
+
+## Documentation Inventory
+
+### Current Features to Document
+
+1. **Project Management**
+   - Create/edit/delete projects
+   - Project list view
+   - Project workspace (default view)
+
+2. **Git Repositories**
+   - Create repositories (bare init, mirror clone)
+   - Smart URL parsing
+   - Repository list
+   - Repository deletion
+
+3. **Repository Workspace**
+   - File browser (tree view)
+   - File viewer (syntax highlighting)
+   - Branch switching
+   - Repository switching
+   - Quick file editing
+
+4. **Git History**
+   - Commit history visualization
+   - Branch graph
+   - Commit details (diff, stats)
+   - Branch filtering
+
+5. **Authentication**
+   - Authentik OAuth2 flow
+   - Session-based auth
+   - User profile
+   - Logout
+
+6. **User Settings**
+   - Theme selection
+   - Git identity
+   - Default editor
+
+7. **Tool Types**
+   - Built-in types (code-server, jupyter)
+   - Custom type creation
+   - Compose template validation
+
+8. **SSH Keys**
+   - Generate key pairs
+   - List/delete keys
+   - Copy public key
+
+## API Endpoints to Document
+
+### Auth
+- GET /auth/login
+- GET /auth/callback
+- GET /auth/me
+- POST /auth/logout
+
+### Projects
+- GET /projects
+- POST /projects
+- GET /projects/{id}
+- PUT /projects/{id}
+- DELETE /projects/{id}
+
+### Repositories
+- GET /projects/{id}/repositories
+- POST /projects/{id}/repositories
+- DELETE /projects/{id}/repositories/{id}
+- GET /projects/{id}/repositories/{id}/files
+- GET /projects/{id}/repositories/{id}/files/content
+- POST /projects/{id}/repositories/{id}/files/content
+- GET /projects/{id}/repositories/{id}/branches
+- GET /projects/{id}/repositories/{id}/history
+- GET /projects/{id}/repositories/{id}/commits/{hash}
+
+### Users
+- GET /users/me
+- PUT /users/me
+- POST /users/me/avatar
+- GET /users/me/config
+- PATCH /users/me/config
+
+### Tool Types
+- GET /tool-types
+- POST /tool-types
+- GET /tool-types/{id}
+- PUT /tool-types/{id}
+- DELETE /tool-types/{id}
+
+### SSH Keys
+- GET /ssh-keys
+- POST /ssh-keys
+- DELETE /ssh-keys/{id}
+
+## Documentation Templates
+
+### Feature Doc Template
+```markdown
+# [Feature Name]
+
+## Overview
+[1-2 sentence description]
+
+## How to Use
+[Step-by-step guide]
+
+## Screenshots
+[If applicable]
+
+## API Reference
+[Links to API docs]
+
+## Configuration
+[Relevant env vars/settings]
+
+## Related
+[Links to related features]
+```
+
+### API Doc Template
+```markdown
+## [METHOD] [PATH]
+
+**Auth:** [Required/Optional]
+
+**Description:** [What it does]
+
+### Request
+[Params/body schema]
+
+### Response
+[Success/error schemas]
+
+### Example
+[Code example]
+```
+
+## Implementation Checklist
+
+For every new feature:
+- [ ] Create feature doc in docs/features/
+- [ ] Document API endpoints in docs/api/
+- [ ] Update README.md features list
+- [ ] Update architecture docs if needed
+- [ ] Add to CHANGELOG.md
+
+## Success Criteria
+
+1. README provides clear project overview
+2. All 8 feature areas have user guides
+3. All API endpoints have documentation
+4. New developer can set up project in < 15 minutes
+5. Deployment guide enables setup without asking questions
+6. Templates exist for future documentation
+7. CONTRIBUTING.md explains documentation requirements

openspec/changes/documentation-overhaul/tasks.md

@@ -0,0 +1,202 @@
+# Documentation Overhaul - Tasks
+
+## Phase 1: README Rewrite
+
+- [ ] **Task 1.1**: Rewrite README.md
+  - Add project overview and description
+  - List all features with brief descriptions
+  - Add quick start section
+  - Add tech stack section
+  - Add links to docs/ directory
+  - Keep testing strategy (or move to docs/testing.md)
+
+- [ ] **Task 1.2**: Create docs/README.md
+  - Documentation index
+  - Link to all doc sections
+  - Quick navigation
+
+## Phase 2: Create Documentation Structure
+
+- [ ] **Task 2.1**: Create docs/ directory structure
+  - mkdir docs/architecture
+  - mkdir docs/features
+  - mkdir docs/api
+  - mkdir docs/deployment
+  - mkdir docs/development
+  - mkdir docs/templates
+
+- [ ] **Task 2.2**: Create documentation templates
+  - docs/templates/feature-doc.md
+  - docs/templates/api-endpoint.md
+  - docs/templates/architecture.md
+
+## Phase 3: Feature Documentation
+
+- [ ] **Task 3.1**: Document Project Management
+  - docs/features/projects.md
+  - Creating/editing/deleting projects
+  - Project list view
+  - Project workspace
+
+- [ ] **Task 3.2**: Document Git Repositories
+  - docs/features/repositories.md
+  - Creating repos (bare init, mirror clone)
+  - Smart URL parsing
+  - Repository management
+
+- [ ] **Task 3.3**: Document Repository Workspace
+  - docs/features/workspace.md
+  - File browser
+  - File viewer
+  - Branch switching
+  - Quick editing
+
+- [ ] **Task 3.4**: Document Git History
+  - docs/features/git-history.md
+  - Commit history view
+  - Branch graph
+  - Commit details
+
+- [ ] **Task 3.5**: Document Authentication
+  - docs/features/auth.md
+  - Authentik OAuth2 flow
+  - Session management
+  - User profile
+
+- [ ] **Task 3.6**: Document User Settings
+  - docs/features/settings.md
+  - Theme selection
+  - Git identity
+  - Preferences
+
+- [ ] **Task 3.7**: Document Tool Types
+  - docs/features/tool-types.md
+  - Built-in types
+  - Custom type creation
+  - Compose templates
+
+- [ ] **Task 3.8**: Document SSH Keys
+  - docs/features/ssh-keys.md
+  - Key generation
+  - Management
+
+## Phase 4: API Documentation
+
+- [ ] **Task 4.1**: Document Auth API
+  - docs/api/auth.md
+  - All auth endpoints
+
+- [ ] **Task 4.2**: Document Projects API
+  - docs/api/projects.md
+  - All project endpoints
+
+- [ ] **Task 4.3**: Document Repositories API
+  - docs/api/repositories.md
+  - All repository endpoints
+  - File operations
+  - History endpoints
+
+- [ ] **Task 4.4**: Document Users API
+  - docs/api/users.md
+  - User profile endpoints
+  - Config endpoints
+
+- [ ] **Task 4.5**: Document Tool Types API
+  - docs/api/tool-types.md
+  - CRUD endpoints
+
+- [ ] **Task 4.6**: Document SSH Keys API
+  - docs/api/ssh-keys.md
+  - Key management endpoints
+
+## Phase 5: Architecture Documentation
+
+- [ ] **Task 5.1**: Create backend architecture doc
+  - docs/architecture/backend.md
+  - Tech stack
+  - Directory structure
+  - Data flow
+  - Auth flow
+
+- [ ] **Task 5.2**: Create frontend architecture doc
+  - docs/architecture/frontend.md
+  - Tech stack
+  - Directory structure
+  - State management
+  - Routing
+
+- [ ] **Task 5.3**: Create database schema doc
+  - docs/architecture/database.md
+  - Entity relationship diagram
+  - Table descriptions
+  - Migration strategy
+
+- [ ] **Task 5.4**: Create deployment architecture doc
+  - docs/architecture/deployment.md
+  - Docker architecture
+  - Traefik routing
+  - Service diagram
+
+## Phase 6: Deployment Guide
+
+- [ ] **Task 6.1**: Create Docker setup guide
+  - docs/deployment/docker.md
+  - Local development setup
+  - Docker compose configuration
+
+- [ ] **Task 6.2**: Create Traefik guide
+  - docs/deployment/traefik.md
+  - Traefik configuration
+  - Routing rules
+  - TLS setup
+
+- [ ] **Task 6.3**: Create Authentik guide
+  - docs/deployment/authentik.md
+  - Provider setup
+  - Application configuration
+  - OAuth2 settings
+
+- [ ] **Task 6.4**: Create environment variables guide
+  - docs/deployment/environment.md
+  - All env vars explained
+  - Required vs optional
+  - Default values
+
+## Phase 7: Development Guide
+
+- [ ] **Task 7.1**: Create setup guide
+  - docs/development/setup.md
+  - Prerequisites
+  - Installation steps
+  - Running locally
+
+- [ ] **Task 7.2**: Move testing strategy
+  - Move from README.md to docs/development/testing.md
+  - Update references
+
+- [ ] **Task 7.3**: Create contributing guide
+  - docs/development/contributing.md
+  - Code style
+  - PR process
+  - Documentation requirements
+
+- [ ] **Task 7.4**: Create quality gates doc
+  - docs/development/quality-gates.md
+  - Linting rules
+  - Type checking
+  - Testing requirements
+
+## Phase 8: Finalization
+
+- [ ] **Task 8.1**: Review all docs
+  - Check for completeness
+  - Check for accuracy
+  - Fix broken links
+
+- [ ] **Task 8.2**: Create CHANGELOG.md
+  - List all features implemented
+  - Link to OpenSpec changes
+
+- [ ] **Task 8.3**: Commit all documentation
+  - Single commit for docs
+  - Conventional commit message

openspec/changes/git-control/.openspec.yaml

@@ -0,0 +1,2 @@
+schema: spec-driven
+created: 2026-05-19

openspec/changes/git-control/design.md

@@ -0,0 +1,273 @@
+# Git Control - Design
+
+## Architecture
+
+```
+Repository Workspace
+├─ Toolbar
+│  ├─ [Fetch] [Pull] [Push]
+│  ├─ [Branch: main ▼] [+ New Branch]
+│  └─ [Commit] [Merge ▼]
+├─ Sidebar
+│  ├─ Repo Selector
+│  ├─ Branch Selector (with management)
+│  └─ File Tree (with status icons)
+│     ├─ 📄 main.py ✏️ (modified)
+│     ├─ 📁 src/
+│     └─ 📄 README.md ✨ (new)
+└─ Main Content
+   ├─ File Viewer (with edit/save)
+   └─ Commit Panel (when files modified)
+      ├─ Changed files list
+      ├─ Commit message input
+      └─ [Commit to main] button
+```
+
+## Git Operations
+
+### Branch Operations
+
+**Create Branch:**
+```
+POST /projects/{id}/repositories/{id}/branches
+{
+  "name": "feature/new-thing",
+  "base_branch": "main"
+}
+```
+
+**Delete Branch:**
+```
+DELETE /projects/{id}/repositories/{id}/branches/{name}
+```
+
+**Checkout Branch:**
+```
+POST /projects/{id}/repositories/{id}/checkout
+{
+  "branch": "feature/new-thing"
+}
+```
+
+### Working Directory Status
+
+**Get Status:**
+```
+GET /projects/{id}/repositories/{id}/status
+```
+
+Response:
+```json
+{
+  "branch": "main",
+  "modified": ["src/main.py", "README.md"],
+  "added": ["new-file.txt"],
+  "deleted": ["old-file.txt"],
+  "untracked": ["temp.log"]
+}
+```
+
+### Commit Operations
+
+**Commit Changes:**
+```
+POST /projects/{id}/repositories/{id}/commits
+{
+  "message": "Update greeting",
+  "author_name": "User",
+  "author_email": "user@example.com",
+  "files": ["src/main.py", "README.md"]
+}
+```
+
+### Remote Operations
+
+**Fetch:**
+```
+POST /projects/{id}/repositories/{id}/fetch
+```
+
+**Pull:**
+```
+POST /projects/{id}/repositories/{id}/pull
+{
+  "branch": "main",
+  "strategy": "merge"
+}
+```
+
+**Push:**
+```
+POST /projects/{id}/repositories/{id}/push
+{
+  "branch": "main"
+}
+```
+
+**Merge:**
+```
+POST /projects/{id}/repositories/{id}/merge
+{
+  "source_branch": "feature/new-thing",
+  "target_branch": "main",
+  "commit_message": "Merge feature into main"
+}
+```
+
+## Backend Implementation
+
+### Git Command Utilities
+
+Extend `src/utils/git_files.py` with:
+- `get_status(repo_path)` - working directory status
+- `create_branch(repo_path, name, base)` - create new branch
+- `delete_branch(repo_path, name)` - delete branch
+- `checkout_branch(repo_path, name)` - switch branch
+- `commit_changes(repo_path, files, message, author)` - commit files
+- `fetch(repo_path)` - fetch from remote
+- `pull(repo_path, branch)` - pull updates
+- `push(repo_path, branch)` - push changes
+- `merge(repo_path, source, target, message)` - merge branches
+
+### Error Handling
+
+All git operations can fail:
+- **Merge conflicts**: Return conflict details, require resolution
+- **Auth failures**: Remote requires authentication
+- **Dirty working tree**: Can't checkout with uncommitted changes
+- **Branch exists**: Can't create duplicate branch
+- **Nothing to commit**: Working tree clean
+
+### Security
+
+- All operations check repository ownership
+- Push/pull requires valid remote URL
+- Commits use authenticated user's identity
+
+## Frontend Implementation
+
+### Workspace Toolbar
+
+Add git action bar above file viewer:
+```
+┌──────────────────────────────────────────────────────┐
+│ [Fetch] [Pull] [Push]  │  Branch: [main ▼] [+ New] │
+│                        │  [Commit ▼] [Merge ▼]      │
+└──────────────────────────────────────────────────────┘
+```
+
+### Branch Management
+
+**Branch Selector Dropdown:**
+- List all branches with current branch highlighted
+- Create new branch option (opens dialog)
+- Delete branch option (with confirmation)
+
+**New Branch Dialog:**
+```
+┌──────────────────────────────┐
+│ Create New Branch            │
+├──────────────────────────────┤
+│ Name: [feature/________]     │
+│ Base: [main ▼]               │
+│                              │
+│ [Create] [Cancel]            │
+└──────────────────────────────┘
+```
+
+### Working Directory Status
+
+**Status Indicators in File Tree:**
+- ✏️ Modified file
+- ✨ New file
+- 🗑️ Deleted file
+- ❓ Untracked file
+
+**Commit Panel (appears when files modified):**
+```
+┌──────────────────────────────┐
+│ Changes (3)                  │
+├──────────────────────────────┤
+│ ✏️ src/main.py               │
+│ ✨ new-file.txt              │
+│ 🗑️ old-file.txt             │
+├──────────────────────────────┤
+│ Commit message:              │
+│ [____________________]       │
+│                              │
+│ [Commit to main]             │
+└──────────────────────────────┘
+```
+
+### Merge Dialog
+
+```
+┌──────────────────────────────┐
+│ Merge Branch                 │
+├──────────────────────────────┤
+│ Source: [feature/xyz ▼]      │
+│ Target: main                 │
+│                              │
+│ Commit message:              │
+│ [Merge feature/xyz into main]│
+│                              │
+│ [Merge] [Cancel]             │
+└──────────────────────────────┘
+```
+
+## Implementation Order
+
+1. **Backend git utilities** - Status, branch, commit, remote operations
+2. **Backend API endpoints** - All git operation endpoints
+3. **Frontend toolbar** - Git action buttons
+4. **Frontend branch management** - Create/delete/checkout
+5. **Frontend status display** - Modified file indicators
+6. **Frontend commit panel** - Commit UI
+7. **Frontend merge dialog** - Merge UI
+8. **Integration** - Wire everything together
+9. **Tests** - Backend + frontend tests
+
+## State Management
+
+### URL State
+```
+/projects/:projectId?repo=:repoId&branch=:branch&path=:path
+```
+
+### React State
+```typescript
+interface GitState {
+  currentBranch: string;
+  branches: Branch[];
+  status: {
+    modified: string[];
+    added: string[];
+    deleted: string[];
+    untracked: string[];
+  };
+  isLoading: boolean;
+  lastOperation: string | null;
+}
+```
+
+## Error Handling
+
+### User-Facing Errors
+- **"Cannot checkout: uncommitted changes"** - Show commit panel
+- **"Merge conflict"** - Show conflict resolution UI
+- **"Push rejected: non-fast-forward"** - Suggest pull first
+- **"Authentication failed"** - Show SSH key settings
+- **"Nothing to commit"** - Working tree clean
+
+### Conflict Resolution (Future)
+For now, show error and abort. Later can add:
+- Diff view of conflicts
+- Manual resolution editor
+- Accept ours/theirs buttons
+
+## Performance Considerations
+
+- **Status updates**: Poll every 5 seconds when viewing workspace
+- **Fetch on load**: Auto-fetch when opening workspace (optional)
+- **Lazy operations**: Don't fetch until user clicks fetch/pull
+- **Progress indicators**: Show for long operations (clone, push, merge)

openspec/changes/git-control/proposal.md

@@ -0,0 +1,44 @@
+# Git Control Features
+
+## Problem
+
+The repository workspace currently provides read-only access to git repositories. Users can browse files, view history, and see branches, but cannot perform git operations like creating branches, committing changes, pushing/pulling, or merging.
+
+## Solution
+
+Add git control capabilities to the repository workspace, allowing users to:
+1. Create and delete branches
+2. Switch between branches (checkout)
+3. Commit changes (for quick edits)
+4. Push changes to remote
+5. Pull/fetch updates from remote
+6. Merge branches
+7. View working directory status
+
+## Benefits
+
+- **Complete workflow**: Users can make small changes without leaving the browser
+- **Quick iterations**: Fix typos, update configs, make small adjustments
+- **Branch management**: Create feature branches, merge when done
+- **Remote sync**: Keep repositories up to date
+- **No external tools needed**: Everything in the browser
+
+## Scope
+
+### What stays:
+- Existing file browser and viewer
+- Git history visualization
+- Repository management (create/delete)
+
+### What's new:
+- Branch CRUD operations
+- Working directory status (modified files)
+- Commit operations
+- Push/pull/fetch
+- Merge capabilities
+- Git action toolbar in workspace
+
+### What changes:
+- Workspace toolbar gets git action buttons
+- File viewer gets "modified" indicators
+- Branch selector gets management options

openspec/changes/git-control/specs/spec.md

@@ -0,0 +1,296 @@
+# Git Control Specification
+
+## Requirements
+
+### Functional Requirements
+
+1. **Branch Management**: Create, delete, list, and switch branches
+2. **Working Directory**: View modified, added, deleted, and untracked files
+3. **Commit Changes**: Stage and commit file changes with message
+4. **Remote Sync**: Fetch, pull, and push to remote repositories
+5. **Merge Branches**: Merge one branch into another
+6. **Status Indicators**: Show file modification status in file tree
+
+### Non-Functional Requirements
+
+1. **Performance**: Git operations complete in < 3 seconds
+2. **Feedback**: Show progress for long operations (push, pull, merge)
+3. **Error Handling**: Clear error messages for all git failures
+4. **Safety**: Confirm destructive operations (delete branch, force push)
+
+## API Specification
+
+### Branch Operations
+
+#### POST /projects/{project_id}/repositories/{repo_id}/branches
+Create a new branch.
+
+**Request:**
+```json
+{
+  "name": "feature/new-thing",
+  "base_branch": "main"
+}
+```
+
+**Response 201:**
+```json
+{
+  "name": "feature/new-thing",
+  "base_commit": "abc123"
+}
+```
+
+**Response 400:** Branch already exists
+
+#### DELETE /projects/{project_id}/repositories/{repo_id}/branches/{branch_name}
+Delete a branch.
+
+**Response 204:** Success
+
+**Response 400:** Cannot delete current branch
+
+#### POST /projects/{project_id}/repositories/{repo_id}/checkout
+Checkout a branch.
+
+**Request:**
+```json
+{
+  "branch": "feature/new-thing"
+}
+```
+
+**Response 200:**
+```json
+{
+  "branch": "feature/new-thing",
+  "commit": "abc123"
+}
+```
+
+**Response 400:** Uncommitted changes
+
+### Status Operations
+
+#### GET /projects/{project_id}/repositories/{repo_id}/status
+Get working directory status.
+
+**Response 200:**
+```json
+{
+  "branch": "main",
+  "ahead": 2,
+  "behind": 1,
+  "modified": ["src/main.py"],
+  "added": ["new-file.txt"],
+  "deleted": [],
+  "untracked": ["temp.log"],
+  "renamed": []
+}
+```
+
+### Commit Operations
+
+#### POST /projects/{project_id}/repositories/{repo_id}/commits
+Commit staged changes.
+
+**Request:**
+```json
+{
+  "message": "Update greeting",
+  "author_name": "User",
+  "author_email": "user@example.com"
+}
+```
+
+**Response 201:**
+```json
+{
+  "hash": "def789",
+  "message": "Update greeting",
+  "branch": "main"
+}
+```
+
+**Response 400:** Nothing to commit
+
+### Remote Operations
+
+#### POST /projects/{project_id}/repositories/{repo_id}/fetch
+Fetch from remote.
+
+**Response 200:**
+```json
+{
+  "success": true,
+  "fetched_branches": ["origin/main", "origin/develop"]
+}
+```
+
+#### POST /projects/{project_id}/repositories/{repo_id}/pull
+Pull updates from remote.
+
+**Request:**
+```json
+{
+  "branch": "main"
+}
+```
+
+**Response 200:**
+```json
+{
+  "success": true,
+  "commits": 3,
+  "files_changed": ["src/main.py", "README.md"]
+}
+```
+
+**Response 409:** Merge conflict
+
+#### POST /projects/{project_id}/repositories/{repo_id}/push
+Push to remote.
+
+**Request:**
+```json
+{
+  "branch": "main"
+}
+```
+
+**Response 200:**
+```json
+{
+  "success": true,
+  "pushed_commits": 2
+}
+```
+
+**Response 400:** Non-fast-forward
+
+### Merge Operations
+
+#### POST /projects/{project_id}/repositories/{repo_id}/merge
+Merge branches.
+
+**Request:**
+```json
+{
+  "source_branch": "feature/new-thing",
+  "target_branch": "main",
+  "commit_message": "Merge feature into main"
+}
+```
+
+**Response 200:**
+```json
+{
+  "success": true,
+  "commit_hash": "abc789",
+  "files_changed": 5
+}
+```
+
+**Response 409:** Merge conflict
+
+## Data Model
+
+### GitStatus
+```typescript
+interface GitStatus {
+  branch: string;
+  ahead: number;
+  behind: number;
+  modified: string[];
+  added: string[];
+  deleted: string[];
+  untracked: string[];
+  renamed: Array<{from: string, to: string}>;
+}
+```
+
+### CommitInfo
+```typescript
+interface CommitInfo {
+  hash: string;
+  message: string;
+  branch: string;
+  author_name: string;
+  author_email: string;
+  date: string;
+}
+```
+
+## Frontend Specification
+
+### Components
+
+**GitToolbar:**
+- Fetch button
+- Pull button (with behind count badge)
+- Push button (with ahead count badge)
+- Branch selector (with create/delete)
+- Commit button (enabled when changes exist)
+- Merge button
+
+**BranchSelector:**
+- Dropdown with all branches
+- Current branch highlighted
+- "Create new branch" option
+- Delete option (with confirmation)
+
+**CommitPanel:**
+- Shows when files are modified
+- Lists changed files with checkboxes
+- Commit message input
+- Commit button
+
+**StatusIndicator:**
+- Small badge on file tree items
+- Shows modification type
+
+### State Management
+
+```typescript
+interface GitControlState {
+  status: GitStatus | null;
+  isLoading: boolean;
+  operations: Array<{
+    type: string;
+    status: 'pending' | 'success' | 'error';
+    message: string;
+  }>;
+}
+```
+
+## Error Handling
+
+| Error Code | Description | User Action |
+|------------|-------------|-------------|
+| DIRTY_WORKING_TREE | Uncommitted changes | Commit or stash changes |
+| MERGE_CONFLICT | Merge failed with conflicts | Resolve conflicts manually |
+| NON_FAST_FORWARD | Push rejected | Pull first |
+| AUTH_FAILED | Remote auth failed | Check SSH keys |
+| BRANCH_EXISTS | Branch already exists | Choose different name |
+| NOTHING_TO_COMMIT | Working tree clean | N/A |
+| CANNOT_DELETE_CURRENT | Can't delete checked out branch | Switch branches first |
+
+## Testing Strategy
+
+### Backend Tests
+- Test branch creation/deletion
+- Test checkout with/without changes
+- Test commit operations
+- Test fetch/pull/push
+- Test merge (fast-forward and conflict)
+- Test error cases
+
+### Frontend Tests
+- Test toolbar buttons
+- Test branch selector
+- Test commit panel
+- Test status indicators
+- Test error handling
+
+### Integration Tests
+- Full workflow: create branch → edit file → commit → push → merge

openspec/changes/git-control/tasks.md

@@ -0,0 +1,142 @@
+# Git Control - Tasks
+
+## Phase 1: Backend Git Utilities
+
+- [x] **Task 1.1**: Extend git utilities
+  - Add to `src/utils/git_control.py`:
+    - `get_status(repo_path)` - working directory status
+    - `create_branch(repo_path, name, base)` - create branch
+    - `delete_branch(repo_path, name)` - delete branch
+    - `checkout_branch(repo_path, name)` - switch branch
+    - `commit_changes(repo_path, message, author)` - commit
+  - Add tests
+
+- [x] **Task 1.2**: Add remote operations
+  - Add to `src/utils/git_control.py`:
+    - `fetch(repo_path)` - fetch from remote
+    - `pull(repo_path, branch)` - pull updates
+    - `push(repo_path, branch)` - push changes
+    - `merge(repo_path, source, target, message)` - merge
+  - Handle errors (conflicts, auth, etc.)
+  - Add tests
+
+## Phase 2: Backend API Endpoints
+
+- [x] **Task 2.1**: Branch management endpoints
+  - POST `/projects/{id}/repositories/{id}/branches` - create
+  - DELETE `/projects/{id}/repositories/{id}/branches/{name}` - delete
+  - POST `/projects/{id}/repositories/{id}/checkout` - checkout
+  - Add to `src/api/git_repositories.py`
+
+- [x] **Task 2.2**: Status endpoint
+  - GET `/projects/{id}/repositories/{id}/status`
+  - Returns working directory status
+
+- [x] **Task 2.3**: Commit endpoint
+  - POST `/projects/{id}/repositories/{id}/commits`
+  - Commits all staged changes
+
+- [x] **Task 2.4**: Remote operation endpoints
+  - POST `/projects/{id}/repositories/{id}/fetch`
+  - POST `/projects/{id}/repositories/{id}/pull`
+  - POST `/projects/{id}/repositories/{id}/push`
+
+- [x] **Task 2.5**: Merge endpoint
+  - POST `/projects/{id}/repositories/{id}/merge`
+  - Handle conflict responses
+
+## Phase 3: Frontend Git Toolbar
+
+- [ ] **Task 3.1**: Create GitToolbar component
+  - Fetch, Pull, Push buttons
+  - Branch selector with count badges
+  - Commit button
+  - Merge button
+  - Add to workspace layout
+
+- [ ] **Task 3.2**: Add status polling
+  - Poll status every 5 seconds
+  - Update toolbar badges (ahead/behind)
+  - Show commit button when changes exist
+
+## Phase 4: Branch Management
+
+- [ ] **Task 4.1**: Enhance BranchSelector
+  - Add "Create new branch" option
+  - Add delete option with confirmation
+  - Show current branch
+  - Call branch API endpoints
+
+- [ ] **Task 4.2**: Create NewBranchDialog
+  - Branch name input
+  - Base branch selector
+  - Create/Cancel buttons
+
+## Phase 5: Commit Workflow
+
+- [ ] **Task 5.1**: Create CommitPanel component
+  - Shows when files are modified
+  - Lists changed files
+  - Commit message input
+  - Commit button
+  - Success/error feedback
+
+- [ ] **Task 5.2**: Add status indicators to FileTree
+  - Modified icon (✏️)
+  - New file icon (✨)
+  - Deleted icon (🗑️)
+  - Untracked icon (❓)
+
+## Phase 6: Remote Operations
+
+- [ ] **Task 6.1**: Implement fetch/pull/push
+  - Wire toolbar buttons to API
+  - Show progress indicators
+  - Handle errors (auth, conflicts, etc.)
+  - Update status after operations
+
+- [ ] **Task 6.2**: Create MergeDialog
+  - Source branch selector
+  - Target branch display
+  - Commit message input
+  - Merge/Cancel buttons
+  - Handle conflicts
+
+## Phase 7: Integration & Polish
+
+- [ ] **Task 7.1**: Wire everything together
+  - Connect toolbar to all APIs
+  - Update workspace state after operations
+  - Refresh file tree on branch switch
+
+- [ ] **Task 7.2**: Add error handling
+  - Show toast notifications for operations
+  - Handle all error cases gracefully
+  - Provide recovery options
+
+- [ ] **Task 7.3**: Add CSS styles
+  - Toolbar layout
+  - Status indicators
+  - Commit panel
+  - Dialogs
+
+- [ ] **Task 7.4**: Run quality gates
+  - Backend: ruff, mypy, pytest
+  - Frontend: typecheck, lint, build
+
+## Phase 8: Testing
+
+- [ ] **Task 8.1**: Backend tests
+  - Test all git operations
+  - Test error cases
+  - Test auth failures
+
+- [ ] **Task 8.2**: Frontend tests
+  - Test toolbar interactions
+  - Test branch management
+  - Test commit workflow
+
+- [ ] **Task 8.3**: Manual testing
+  - Create branch → edit → commit → push → merge workflow
+  - Test error scenarios
+  - Test with multiple repos