feat: Major directory reorganization and cleanup

Reorganized project structure for better maintainability and reduced
disk usage by 95.9% (11 GB -> 451 MB).

Directory Reorganization (85% reduction in root files):
- Created docs/ with subdirectories (deployment, testing, database, etc.)
- Created infrastructure/vpn-configs/ for VPN scripts
- Moved 90+ files from root to organized locations
- Archived obsolete documentation (context system, offline mode, zombie debugging)
- Moved all test files to tests/ directory
- Root directory: 119 files -> 18 files

Disk Cleanup (10.55 GB recovered):
- Deleted Rust build artifacts: 9.6 GB (target/ directories)
- Deleted Python virtual environments: 161 MB (venv/ directories)
- Deleted Python cache: 50 KB (__pycache__/)

New Structure:
- docs/ - All documentation organized by category
- docs/archives/ - Obsolete but preserved documentation
- infrastructure/ - VPN configs and SSH setup
- tests/ - All test files consolidated
- logs/ - Ready for future logs

Benefits:
- Cleaner root directory (18 vs 119 files)
- Logical organization of documentation
- 95.9% disk space reduction
- Faster navigation and discovery
- Better portability (build artifacts excluded)

Build artifacts can be regenerated:
- Rust: cargo build --release (5-15 min per project)
- Python: pip install -r requirements.txt (2-3 min)

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

scripts/example_credential_import.py

@@ -0,0 +1,158 @@
+"""
+Example: Import credentials from a client project directory.
+
+This script demonstrates a real-world use case for the credential scanner:
+importing credentials from a client's project directory into the ClaudeTools
+credential vault with automatic encryption.
+
+Usage:
+    python example_credential_import.py /path/to/client/project [--client-id UUID]
+"""
+
+import argparse
+import logging
+import sys
+from pathlib import Path
+
+from api.database import SessionLocal
+from api.utils.credential_scanner import (
+    scan_for_credential_files,
+    parse_credential_file,
+    import_credentials_to_db,
+    scan_and_import_credentials,
+)
+
+# Configure logging
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(levelname)s - %(message)s'
+)
+logger = logging.getLogger(__name__)
+
+
+def preview_credentials(base_path: str):
+    """Preview credentials that would be imported without actually importing."""
+    logger.info(f"Scanning for credentials in: {base_path}")
+
+    # Find credential files
+    files = scan_for_credential_files(base_path)
+
+    if not files:
+        logger.warning("No credential files found")
+        return []
+
+    logger.info(f"\nFound {len(files)} credential file(s):")
+    for file_path in files:
+        logger.info(f"  - {file_path}")
+
+    # Parse and preview
+    all_credentials = []
+    for file_path in files:
+        credentials = parse_credential_file(file_path)
+        all_credentials.extend(credentials)
+
+        logger.info(f"\n{Path(file_path).name}:")
+        for cred in credentials:
+            logger.info(f"  Service: {cred.get('service_name')}")
+            logger.info(f"  Type: {cred.get('credential_type')}")
+            if cred.get('username'):
+                logger.info(f"  Username: {cred.get('username')}")
+            logger.info("")
+
+    logger.info(f"Total credentials found: {len(all_credentials)}")
+    return all_credentials
+
+
+def import_with_confirmation(base_path: str, client_id: str = None):
+    """Import credentials with user confirmation."""
+
+    # Preview first
+    credentials = preview_credentials(base_path)
+
+    if not credentials:
+        logger.info("No credentials to import")
+        return
+
+    # Ask for confirmation
+    logger.info("\n" + "=" * 60)
+    response = input(f"Import {len(credentials)} credential(s) to database? (yes/no): ")
+
+    if response.lower() not in ['yes', 'y']:
+        logger.info("Import cancelled")
+        return
+
+    # Import to database
+    db = SessionLocal()
+    try:
+        logger.info("\nImporting credentials...")
+        results = scan_and_import_credentials(
+            base_path=base_path,
+            db=db,
+            client_id=client_id,
+            user_id="manual_import",
+            ip_address=None
+        )
+
+        logger.info("\n" + "=" * 60)
+        logger.info("IMPORT COMPLETE")
+        logger.info("=" * 60)
+        logger.info(f"Files scanned: {results['files_found']}")
+        logger.info(f"Credentials parsed: {results['credentials_parsed']}")
+        logger.info(f"Credentials imported: {results['credentials_imported']}")
+
+        if results['credentials_imported'] < results['credentials_parsed']:
+            logger.warning(
+                f"Warning: {results['credentials_parsed'] - results['credentials_imported']} "
+                "credential(s) failed to import. Check logs for details."
+            )
+
+    except Exception as e:
+        logger.error(f"Import failed: {str(e)}", exc_info=True)
+        raise
+    finally:
+        db.close()
+
+
+def main():
+    """Main entry point."""
+    parser = argparse.ArgumentParser(
+        description="Import credentials from a directory into ClaudeTools credential vault"
+    )
+    parser.add_argument(
+        'path',
+        type=str,
+        help='Path to directory containing credential files'
+    )
+    parser.add_argument(
+        '--client-id',
+        type=str,
+        help='UUID of client to associate credentials with (optional)',
+        default=None
+    )
+    parser.add_argument(
+        '--preview',
+        action='store_true',
+        help='Preview credentials without importing'
+    )
+
+    args = parser.parse_args()
+
+    # Validate path
+    path = Path(args.path)
+    if not path.exists():
+        logger.error(f"Path does not exist: {args.path}")
+        sys.exit(1)
+
+    if not path.is_dir():
+        logger.error(f"Path is not a directory: {args.path}")
+        sys.exit(1)
+
+    # Preview or import
+    if args.preview:
+        preview_credentials(str(path))
+    else:
+        import_with_confirmation(str(path), args.client_id)
+
+
+if __name__ == "__main__":
+    main()