feat: add 'clean' command to remove stale index entries

[echobt]

This PR adds a new vgrep clean command to identify and remove entries from the database that correspond to files that no longer exist on the filesystem.

Features

• vgrep clean: Scans the database for stale entries and prompts for removal.
• vgrep clean --dry-run: Shows which entries would be removed without making changes.
• vgrep clean --force: Removes stale entries without interactive confirmation (useful for scripts).

Usage

# Preview what will be cleaned
vgrep clean --dry-run

# Interactive cleanup
vgrep clean

# Force cleanup (non-interactive)
vgrep clean --force

Verification

I reproduced the issue by manually inserting stale entries into the database and verified that:

1. vgrep clean --dry-run correctly identifies them.
2. vgrep clean --force successfully removes them.
3. vgrep clean (interactive) works when running in a terminal.