gitnexus clean

Delete GitNexus indexes and unregister repositories

The clean command removes the .gitnexus/ index directory from a repository and unregisters it from the global registry.

Usage

gitnexus clean [options]

Options

force · boolean · default: "false"

Skip confirmation prompt and delete immediately.

Flag: -f, --force

all · boolean · default: "false"

Delete indexes for all registered repositories (instead of just the current one).

Flag: --all

Examples

Clean Current Repository

Run from within a git repository:

cd my-project
gitnexus clean

Output:

This will delete the GitNexus index for: my-project
   Path: /Users/dev/my-project/.gitnexus

Run with --force to confirm deletion.

Confirm:

gitnexus clean --force

Output:

Deleted: /Users/dev/my-project/.gitnexus

Clean All Repositories

gitnexus clean --all

Output:

This will delete GitNexus indexes for 3 repo(s):
  - my-app (/Users/dev/my-app)
  - backend (/Users/dev/backend)
  - frontend (/Users/dev/frontend)

Run with --force to confirm deletion.

Confirm:

gitnexus clean --all --force

Output:

Deleted: my-app (/Users/dev/my-app/.gitnexus)
Deleted: backend (/Users/dev/backend/.gitnexus)
Deleted: frontend (/Users/dev/frontend/.gitnexus)

What Gets Deleted

Repository Index

The entire .gitnexus/ directory is removed:

.gitnexus/
├── db/              # KuzuDB graph database
├── wiki/            # Generated documentation (if exists)
└── meta.json        # Index metadata

Global Registry Entry

The repository is removed from ~/.gitnexus/registry.json.

What Stays

• Source code (untouched)
• .gitignore entry (harmless if index is deleted)
• AGENTS.md and CLAUDE.md files (can be manually deleted)
• Agent skills in .claude/skills/ (per-repo, can be manually deleted)

Use Cases

Free Disk Space

Indexes can grow to 100-500 MB for large repositories. Use clean to reclaim space:

gitnexus clean --force

Re-index After Corruption

If the index is corrupted:

gitnexus clean --force
gitnexus analyze

Remove All Indexes Before Uninstalling

gitnexus clean --all --force
npm uninstall -g gitnexus

Safety

Confirmation Required

By default, clean shows what will be deleted and requires --force to proceed.

No Impact on Source Code

Only the .gitnexus/ directory is deleted. Your source code is never touched.

Re-indexing

You can always re-index after cleaning:

gitnexus clean --force
gitnexus analyze  # Rebuild index

Troubleshooting

”No indexed repository found in this directory”

You’re not in a repository that has been indexed.

Solution:

cd /path/to/indexed/repo
gitnexus clean

Or use --all to clean all indexed repos:

gitnexus clean --all --force

Permission Denied

The .gitnexus/ directory may be locked by another process.

Solution:

1. Stop any running gitnexus serve or MCP servers
2. Close your editor
3. Retry:
   gitnexus clean --force
   

Failed to Delete (Partial Deletion)

If deletion fails partway through:

# Manually remove the directory
rm -rf .gitnexus/

# Unregister from global registry
gitnexus clean --force  # Will skip deletion, only unregister

Impact on MCP

After cleaning a repository:

• MCP tools will no longer see it in list_repos
• Queries targeting that repo will fail
• The web UI will not show it

Re-run gitnexus analyze to restore MCP access.

See Also

• gitnexus list — View all indexed repositories
• gitnexus analyze — Re-index after cleaning
• gitnexus status — Check index status