cursor-codebase-indexing

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 <[e-mail]>
compatible-with	claude-code, codex, openclaw
tags	["saas","cursor","cursor-codebase"]

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:

# .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:

# .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:

# 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:

# .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:

# 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
• Ignore Files
• Secure Codebase Indexing