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Syntax

gitnexus clean

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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.

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Options

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--force
boolean
Skip confirmation prompt and delete immediately.
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--all
boolean
Clean all indexed repositories instead of just the current one.Requires --force for confirmation.

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Usage Examples

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Clean current repository (with prompt)

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.

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Clean current repository (skip prompt)

gitnexus clean --force
Output: 
Deleted: /Users/dev/projects/my-app/.gitnexus

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Clean all repositories (with prompt)

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.

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Clean all repositories (skip prompt)

gitnexus clean --all --force
Output: 
Deleted: my-app (/Users/dev/projects/my-app/.gitnexus)
Deleted: backend-api (/Users/dev/projects/backend-api/.gitnexus)

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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)

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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

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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.

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When to Use

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Free up disk space

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

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Reset corrupted index

If the index is corrupted or incomplete: 
gitnexus clean --force
gitnexus analyze

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Before archiving a repository

gitnexus clean --force
tar -czf my-app.tar.gz my-app/

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Clean all old indexes

Remove all indexes at once: 
gitnexus clean --all --force

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After Cleaning

To re-index a repository: 
gitnexus analyze
The MCP server and HTTP server will automatically discover the new index (no restart needed).

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