> ## 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 index for current repository

## Syntax

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

## Description

Removes the `.gitnexus/` index from the current repository and unregisters it from the global registry.

By default, the command prompts for confirmation before deleting. Use `--force` to skip the prompt.

## Options

<ParamField path="--force" type="boolean" optional>
  Skip confirmation prompt and delete immediately.
</ParamField>

<ParamField path="--all" type="boolean" optional>
  Clean all indexed repositories instead of just the current one.

  Requires `--force` for confirmation.
</ParamField>

## Usage Examples

### Clean current repository (with prompt)

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

Output:

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

Run with --force to confirm deletion.
```

### Clean current repository (skip prompt)

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

Output:

```
Deleted: /Users/dev/projects/my-app/.gitnexus
```

### Clean all repositories (with prompt)

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

Output:

```
This will delete GitNexus indexes for 2 repo(s):
  - my-app (/Users/dev/projects/my-app/.gitnexus)
  - backend-api (/Users/dev/projects/backend-api/.gitnexus)

Run with --force to confirm deletion.
```

### Clean all repositories (skip prompt)

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

Output:

```
Deleted: my-app (/Users/dev/projects/my-app/.gitnexus)
Deleted: backend-api (/Users/dev/projects/backend-api/.gitnexus)
```

## What Gets Deleted

* `.gitnexus/` directory in the repository
  * KuzuDB database files
  * Full-text search indexes
  * Embedding data
  * Wiki output
  * Metadata files
* Entry in global registry (`~/.gitnexus/registry.json`)

## What Doesn't Get Deleted

* Source code (only the index is removed)
* AI context files (`AGENTS.md`, `CLAUDE.md`) — these are kept
* Global skills in `~/.claude/skills/` or `~/.cursor/skills/`
* MCP configuration files

## Safety

The clean command is **safe** — it only deletes GitNexus's own data. Your source code and git history are never touched.

The `.gitnexus/` directory is automatically gitignored by the analyze command, so indexes are never committed to version control.

## When to Use

### Free up disk space

Indexes can be large for big repositories (100MB+ for large codebases). Clean unused indexes:

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

### Reset corrupted index

If the index is corrupted or incomplete:

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

### Before archiving a repository

```bash theme={null}
gitnexus clean --force
tar -czf my-app.tar.gz my-app/
```

### Clean all old indexes

Remove all indexes at once:

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

## After Cleaning

To re-index a repository:

```bash theme={null}
gitnexus analyze
```

The MCP server and HTTP server will automatically discover the new index (no restart needed).

## Related Commands

* [`gitnexus analyze`](/api/commands/analyze) — Rebuild the index
* [`gitnexus status`](/api/commands/status) — Check index status
* [`gitnexus list`](/api/commands/list) — List all indexed repositories