feat: Add arbitrary directory project storage with registry system

This major update replaces the fixed `generations/` directory with support
for storing projects in any directory on the filesystem. Projects are now
tracked via a cross-platform registry system.

## New Features

### Project Registry (`registry.py`)
- Cross-platform registry storing project name-to-path mappings
- Platform-specific config locations:
  - Windows: %APPDATA%\autonomous-coder\projects.json
  - macOS: ~/Library/Application Support/autonomous-coder/projects.json
  - Linux: ~/.config/autonomous-coder/projects.json
- POSIX path format for cross-platform compatibility
- File locking for concurrent access safety (fcntl/msvcrt)
- Atomic writes via temp file + rename to prevent corruption
- Fixed Windows file locking issue with tempfile.mkstemp()

### Filesystem Browser API (`server/routers/filesystem.py`)
- REST endpoints for browsing directories server-side
- Cross-platform support with blocked system paths:
  - Windows: C:\Windows, Program Files, ProgramData, etc.
  - macOS: /System, /Library, /private, etc.
  - Linux: /etc, /var, /usr, /bin, etc.
- Universal blocked paths: .ssh, .aws, .gnupg, .docker, etc.
- Hidden file detection (Unix dot-prefix + Windows attributes)
- UNC path blocking for security
- Windows drive enumeration via ctypes
- Directory creation with validation
- Added `has_children` field to DirectoryEntry schema

### UI Folder Browser (`ui/src/components/FolderBrowser.tsx`)
- React component for selecting project directories
- Breadcrumb navigation with clickable segments
- Windows drive selector
- New folder creation inline
- Fixed text visibility with explicit color values

## Updated Components

### Server Routers
- `projects.py`: Uses registry instead of fixed generations/ directory
- `agent.py`: Uses registry for project path lookups
- `features.py`: Uses registry for database path resolution
- `spec_creation.py`: Uses registry for WebSocket project resolution

### Process Manager (`server/services/process_manager.py`)
- Fixed sandbox issue: subprocess now uses project_dir as cwd
- This allows the Claude SDK sandbox to access external project directories

### Schemas (`server/schemas.py`)
- Added `has_children` to DirectoryEntry
- Added `in_progress` to ProjectStats
- Added path field to ProjectSummary and ProjectDetail

### UI Components
- `NewProjectModal.tsx`: Multi-step wizard with folder selection
- Added clarifying text about subfolder creation
- Fixed text color visibility issues

### API Client (`ui/src/lib/api.ts`)
- Added filesystem API functions (listDirectory, createDirectory)
- Fixed Windows path splitting for directory creation

### Documentation
- Updated CLAUDE.md with registry system details
- Updated command examples for absolute paths

## Security Improvements
- Blocked `.` and `..` in directory names to prevent traversal
- Added path blocking check in project creation
- UNC path blocking throughout filesystem API

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

CLAUDE.md

@@ -39,8 +39,9 @@ pip install -r requirements.txt
 # Run the main CLI launcher
 python start.py
 
-# Run agent directly for a specific project
-python autonomous_agent_demo.py --project-dir PROJECT_NAME
+# Run agent directly for a project (use absolute path or registered name)
+python autonomous_agent_demo.py --project-dir C:/Projects/my-app
+python autonomous_agent_demo.py --project-dir my-app  # if registered
 ```
 
 ### React UI (in ui/ directory)
@@ -66,6 +67,29 @@ npm run lint     # Run ESLint
 - `security.py` - Bash command allowlist validation (ALLOWED_COMMANDS whitelist)
 - `prompts.py` - Prompt template loading with project-specific fallback
 - `progress.py` - Progress tracking, database queries, webhook notifications
+- `registry.py` - Project registry for mapping names to paths (cross-platform)
+
+### Project Registry
+
+Projects can be stored in any directory. The registry (`projects.json`) maps project names to paths:
+- **Windows**: `%APPDATA%\autonomous-coder\projects.json`
+- **macOS**: `~/Library/Application Support/autonomous-coder/projects.json`
+- **Linux**: `~/.config/autonomous-coder/projects.json`
+
+The registry uses:
+- POSIX path format (forward slashes) for cross-platform compatibility
+- File locking for concurrent access safety
+- Atomic writes (temp file + rename) to prevent corruption
+
+### Server API (server/)
+
+The FastAPI server provides REST endpoints for the UI:
+
+- `server/routers/projects.py` - Project CRUD with registry integration
+- `server/routers/features.py` - Feature management
+- `server/routers/agent.py` - Agent control (start/stop/pause/resume)
+- `server/routers/filesystem.py` - Filesystem browser API with security controls
+- `server/routers/spec_creation.py` - WebSocket for interactive spec creation
 
 ### Feature Management
 
@@ -90,14 +114,17 @@ MCP tools available to the agent:
 - `src/hooks/useProjects.ts` - React Query hooks for API calls
 - `src/lib/api.ts` - REST API client
 - `src/lib/types.ts` - TypeScript type definitions
+- `src/components/FolderBrowser.tsx` - Server-side filesystem browser for project folder selection
+- `src/components/NewProjectModal.tsx` - Multi-step project creation wizard
 
 ### Project Structure for Generated Apps
 
-Generated projects are stored in `generations/PROJECT_NAME/` with:
+Projects can be stored in any directory (registered in `projects.json`). Each project contains:
 - `prompts/app_spec.txt` - Application specification (XML format)
 - `prompts/initializer_prompt.md` - First session prompt
 - `prompts/coding_prompt.md` - Continuation session prompt
 - `features.db` - SQLite database with feature test cases
+- `.agent.lock` - Lock file to prevent multiple agent instances
 
 ### Security Model
 
@@ -116,7 +143,7 @@ Defense-in-depth approach configured in `client.py`:
 
 ### Prompt Loading Fallback Chain
 
-1. Project-specific: `generations/{project}/prompts/{name}.md`
+1. Project-specific: `{project_dir}/prompts/{name}.md`
 2. Base template: `.claude/templates/{name}.template.md`
 
 ### Agent Session Flow