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>

server/routers/agent.py

@@ -3,6 +3,7 @@ Agent Router
 ============
 
 API endpoints for agent control (start/stop/pause/resume).
+Uses project registry for path lookups.
 """
 
 import re
@@ -13,21 +14,16 @@ from fastapi import APIRouter, HTTPException
 from ..schemas import AgentStatus, AgentActionResponse
 from ..services.process_manager import get_manager
 
-# Lazy import to avoid sys.path manipulation at module level
-_GENERATIONS_DIR = None
 
+def _get_project_path(project_name: str) -> Path:
+    """Get project path from registry."""
+    import sys
+    root = Path(__file__).parent.parent.parent
+    if str(root) not in sys.path:
+        sys.path.insert(0, str(root))
 
-def _get_generations_dir():
-    """Lazy import of GENERATIONS_DIR."""
-    global _GENERATIONS_DIR
-    if _GENERATIONS_DIR is None:
-        import sys
-        root = Path(__file__).parent.parent.parent
-        if str(root) not in sys.path:
-            sys.path.insert(0, str(root))
-        from start import GENERATIONS_DIR
-        _GENERATIONS_DIR = GENERATIONS_DIR
-    return _GENERATIONS_DIR
+    from registry import get_project_path
+    return get_project_path(project_name)
 
 
 router = APIRouter(prefix="/api/projects/{project_name}/agent", tags=["agent"])
@@ -49,12 +45,15 @@ def validate_project_name(name: str) -> str:
 def get_project_manager(project_name: str):
     """Get the process manager for a project."""
     project_name = validate_project_name(project_name)
-    project_dir = _get_generations_dir() / project_name
+    project_dir = _get_project_path(project_name)
+
+    if not project_dir:
+        raise HTTPException(status_code=404, detail=f"Project '{project_name}' not found in registry")
 
     if not project_dir.exists():
-        raise HTTPException(status_code=404, detail=f"Project '{project_name}' not found")
+        raise HTTPException(status_code=404, detail=f"Project directory not found: {project_dir}")
 
-    return get_manager(project_name, ROOT_DIR)
+    return get_manager(project_name, project_dir, ROOT_DIR)
 
 
 @router.get("/status", response_model=AgentStatus)