cursor-codebase-indexing

by jeremylongshore

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SKILL.md About

---
name: cursor-codebase-indexing
description: 'Set up and optimize Cursor codebase indexing for semantic code search
  and @Codebase queries.

Triggers on "cursor index", "codebase indexing", "index codebase", "cursor semantic
  search",

"@codebase", "cursor embeddings".

'
allowed-tools: Read, Write, Edit, Bash(cmd:*)
version: 1.0.0
license: MIT
author: Jeremy Longshore <jeremy@intentsolutions.io>
tags:
- saas
- cursor
- cursor-codebase
compatibility: Designed for Claude Code, also compatible with Codex and OpenClaw
---
# Cursor Codebase Indexing

Set up and optimize Cursor's codebase indexing system. Indexing creates embeddings of your code, enabling `@Codebase` semantic search and improving AI context awareness across Chat, Composer, and Agent mode.

## How Indexing Works

```
Your Code Files
      │
      ▼
  Syntax Chunking ─── splits files into meaningful code blocks
      │
      ▼
  Embedding Generation ─── converts chunks to vector representations
      │
      ▼
  Vector Storage (Turbopuffer) ─── cloud-hosted nearest-neighbor search
      │
      ▼
  @Codebase Query ─── your question → embedding → similarity search → relevant chunks
```

### Key Architecture Details

- **Merkle tree** for change detection: only modified files are re-indexed (every 10 minutes)
- **No plaintext storage**: code is not stored server-side; only embeddings and obfuscated metadata
- **Privacy Mode compatible**: with Privacy Mode on, embeddings are computed without retaining source code
- Indexing runs in the background; small projects complete in seconds, large projects (50K+ files) may take hours initially

## Initial Setup

1. Open your project in Cursor
2. Indexing starts automatically on first open
3. Check status: look at the bottom status bar for "Indexing..." indicator
4. View indexed files: `Cursor Settings` > `Features` > `Codebase Indexing` > `View included files`

### Verify Indexing Status

The status bar shows:
- **"Indexing..."** with progress indicator -- initial indexing in progress
- **"Indexed"** -- indexing complete, `@Codebase` queries are available
- No indicator -- indexing may be disabled or not started

## Configuration

### .cursorignore

Exclude files from indexing and AI features. Place in project root. Uses `.gitignore` syntax:

```gitignore
# .cursorignore

# Build artifacts (large, not useful for AI context)
dist/
build/
out/
.next/
target/

# Dependencies
node_modules/
vendor/
venv/
.venv/

# Generated files
*.min.js
*.min.css
*.bundle.js
*.map
*.lock

# Large data files
*.csv
*.sql
*.sqlite
*.parquet
fixtures/
seed-data/

# Secrets (defense in depth -- also use .gitignore)
.env*
**/secrets/
**/credentials/
```

### .cursorindexingignore

Exclude files from indexing only but keep them accessible to AI features when explicitly referenced:

```gitignore
# .cursorindexingignore

# Large test fixtures -- don't index, but allow @Files reference
tests/fixtures/
e2e/recordings/

# Documentation build output
docs/.vitepress/dist/
```

**Difference:** `.cursorignore` hides files from both indexing and AI features. `.cursorindexingignore` only excludes from the index; files can still be referenced via `@Files`.

### Default Exclusions

Cursor automatically excludes everything in `.gitignore`. You only need `.cursorignore` for files tracked by git that you want to exclude from AI.

## Using the Index

### @Codebase Queries

Ask semantic questions about your entire codebase:

```
@Codebase where is user authentication handled?

@Codebase show me all API endpoints that accept file uploads

@Codebase how does the payment processing flow work?

@Codebase find all places where we connect to Redis
```

`@Codebase` performs a nearest-neighbor search using your question's embedding. It returns the most semantically similar code chunks, even if they do not contain the exact keywords you used.

### @Codebase vs @Files vs Text Search

| Method | When to Use | Context Cost |
|--------|------------|--------------|
| `@Codebase` | Discovery -- you don't know which files | High (many chunks) |
| `@Files` | You know exactly which file | Low (one file) |
| `@Folders` | You know the directory | Medium-High |
| `Ctrl+Shift+F` | Exact text/regex match | N/A (editor search) |

Use `@Codebase` for discovery, then switch to `@Files` once you know where the code lives.

## Optimization for Large Projects

### Monorepo Strategy

For monorepos with many packages, open the specific package directory instead of the root:

```bash
# Instead of opening the entire monorepo:
cursor /path/to/monorepo           # Indexes everything -- slow

# Open the specific package:
cursor /path/to/monorepo/packages/api   # Indexes only this package -- fast
```

Or use `.cursorignore` at the root to exclude packages you are not actively working on:

```gitignore
# .cursorignore -- monorepo, focus on api and shared
packages/web/
packages/mobile/
packages/admin/
# packages/api/    ← not listed, so it IS indexed
# packages/shared/ ← not listed, so it IS indexed
```

### Re-Indexing

If search results are stale or indexing appears stuck:

1. `Cmd+Shift+P` > `Cursor: Resync Index`
2. Wait for status bar to show indexing progress
3. If that fails, delete the local cache:
   - macOS: `~/Library/Application Support/Cursor/Cache/`
   - Linux: `~/.config/Cursor/Cache/`
   - Windows: `%APPDATA%\Cursor\Cache\`
4. Restart Cursor and allow full re-index

### File Watcher Limits (Linux)

On Linux, large projects may hit the file watcher limit:

```bash
# Check current limit
cat /proc/sys/fs/inotify/max_user_watches

# Increase (temporary)
sudo sysctl fs.inotify.max_user_watches=524288

# Increase (permanent)
echo "fs.inotify.max_user_watches=524288" | sudo tee -a /etc/sysctl.conf
sudo sysctl -p
```

## Enterprise Considerations

- **Data residency**: Embeddings are stored in Turbopuffer (cloud). Obfuscated filenames and no plaintext code, but metadata exists
- **Privacy Mode**: With Privacy Mode on, embeddings are computed with zero data retention at the provider
- **Air-gapped environments**: Indexing requires network access to Cursor's embedding API. Not available offline
- **Indexing scope**: Only files in the currently open workspace are indexed. Closing a project removes its index from active queries

## Troubleshooting

| Symptom | Cause | Fix |
|---------|-------|-----|
| @Codebase returns no results | Index not built | Wait for "Indexed" in status bar |
| Search misses known files | File in .gitignore or .cursorignore | Check ignore files |
| Indexing stuck at N% | Large project or network issue | Resync index via Command Palette |
| Stale results after refactor | Index not yet updated | Wait 10 min or manual resync |
| High CPU during indexing | Initial embedding computation | Normal for first run; subsides |

## Resources

- [Codebase Indexing Docs](https://docs.cursor.com/context/codebase-indexing)
- [Ignore Files](https://docs.cursor.com/context/ignore-files)
- [Secure Codebase Indexing](https://cursor.com/blog/secure-codebase-indexing)