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>

autonomous_agent_demo.py

@@ -8,8 +8,14 @@ This script implements the two-agent pattern (initializer + coding agent) and
 incorporates all the strategies from the long-running agents guide.
 
 Example Usage:
-    python autonomous_agent_demo.py --project-dir ./claude_clone_demo
-    python autonomous_agent_demo.py --project-dir ./claude_clone_demo --max-iterations 5
+    # Using absolute path directly
+    python autonomous_agent_demo.py --project-dir C:/Projects/my-app
+
+    # Using registered project name (looked up from registry)
+    python autonomous_agent_demo.py --project-dir my-app
+
+    # Limit iterations for testing
+    python autonomous_agent_demo.py --project-dir my-app --max-iterations 5
 """
 
 import argparse
@@ -24,6 +30,7 @@ from dotenv import load_dotenv
 load_dotenv()
 
 from agent import run_autonomous_agent
+from registry import get_project_path
 
 
 # Configuration
@@ -38,17 +45,17 @@ def parse_args() -> argparse.Namespace:
         formatter_class=argparse.RawDescriptionHelpFormatter,
         epilog="""
 Examples:
-  # Start fresh project
-  python autonomous_agent_demo.py --project-dir ./claude_clone
+  # Use absolute path directly
+  python autonomous_agent_demo.py --project-dir C:/Projects/my-app
+
+  # Use registered project name (looked up from registry)
+  python autonomous_agent_demo.py --project-dir my-app
 
   # Use a specific model
-  python autonomous_agent_demo.py --project-dir ./claude_clone --model claude-sonnet-4-5-20250929
+  python autonomous_agent_demo.py --project-dir my-app --model claude-sonnet-4-5-20250929
 
   # Limit iterations for testing
-  python autonomous_agent_demo.py --project-dir ./claude_clone --max-iterations 5
-
-  # Continue existing project
-  python autonomous_agent_demo.py --project-dir ./claude_clone
+  python autonomous_agent_demo.py --project-dir my-app --max-iterations 5
 
 Authentication:
   Uses Claude CLI credentials from ~/.claude/.credentials.json
@@ -58,9 +65,9 @@ Authentication:
 
     parser.add_argument(
         "--project-dir",
-        type=Path,
-        default=Path("./autonomous_demo_project"),
-        help="Directory for the project (default: generations/autonomous_demo_project). Relative paths automatically placed in generations/ directory.",
+        type=str,
+        required=True,
+        help="Project directory path (absolute) or registered project name",
     )
 
     parser.add_argument(
@@ -87,16 +94,26 @@ def main() -> None:
     # Note: Authentication is handled by start.bat/start.sh before this script runs.
     # The Claude SDK auto-detects credentials from ~/.claude/.credentials.json
 
-    # Automatically place projects in generations/ directory unless already specified
-    project_dir = args.project_dir
-    if not str(project_dir).startswith("generations/"):
-        # Convert relative paths to be under generations/
-        if project_dir.is_absolute():
-            # If absolute path, use as-is
-            pass
+    # Resolve project directory:
+    # 1. If absolute path, use as-is
+    # 2. Otherwise, look up from registry by name
+    project_dir_input = args.project_dir
+    project_dir = Path(project_dir_input)
+
+    if project_dir.is_absolute():
+        # Absolute path provided - use directly
+        if not project_dir.exists():
+            print(f"Error: Project directory does not exist: {project_dir}")
+            return
+    else:
+        # Treat as a project name - look up from registry
+        registered_path = get_project_path(project_dir_input)
+        if registered_path:
+            project_dir = registered_path
         else:
-            # Prepend generations/ to relative paths
-            project_dir = Path("generations") / project_dir
+            print(f"Error: Project '{project_dir_input}' not found in registry")
+            print("Use an absolute path or register the project first.")
+            return
 
     try:
         # Run the agent (MCP server handles feature database)