> ## Documentation Index
> Fetch the complete documentation index at: https://mintlify.com/abhigyanpatwari/GitNexus/llms.txt
> Use this file to discover all available pages before exploring further.

# 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

```bash theme={null}
gitnexus clean [options]
```

## Options

<ParamField query="force" type="boolean" default="false">
  Skip confirmation prompt and delete immediately.

  **Flag:** `-f, --force`
</ParamField>

<ParamField query="all" type="boolean" default="false">
  Delete indexes for **all** registered repositories (instead of just the current one).

  **Flag:** `--all`
</ParamField>

## Examples

### Clean Current Repository

Run from within a git repository:

```bash theme={null}
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:**

```bash theme={null}
gitnexus clean --force
```

**Output:**

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

### Clean All Repositories

```bash theme={null}
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:**

```bash theme={null}
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:

```bash theme={null}
gitnexus clean --force
```

### Re-index After Corruption

If the index is corrupted:

```bash theme={null}
gitnexus clean --force
gitnexus analyze
```

### Remove All Indexes Before Uninstalling

```bash theme={null}
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:

```bash theme={null}
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:**

```bash theme={null}
cd /path/to/indexed/repo
gitnexus clean
```

Or use `--all` to clean all indexed repos:

```bash theme={null}
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:
   ```bash theme={null}
   gitnexus clean --force
   ```

### Failed to Delete (Partial Deletion)

If deletion fails partway through:

```bash theme={null}
# 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](/cli/list) — View all indexed repositories
* [gitnexus analyze](/cli/analyze) — Re-index after cleaning
* [gitnexus status](/cli/status) — Check index status