Agent skill

Cursor Indexing Issues

by jeremylongshore in jeremylongshore/tons-of-skills-marketplace

Troubleshoot Cursor codebase indexing: stuck indexing, empty search, @codebase failures, and performance issues.

MITAuto-check: notesDevelopment

Install Cursor Indexing Issues

skills CLI
$ npx skills add jeremylongshore/tons-of-skills-marketplace --skill cursor-indexing-issues -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install jeremylongshore/tons-of-skills-marketplace cursor-indexing-issues --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/jeremylongshore/tons-of-skills-marketplace.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/.curated/cursor-indexing-issues .claude/skills/cursor-indexing-issues && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
cursor-indexing-issues
GitHub stars
2.8k
Token cost
~2k tokens
SKILL.md length
746 words
Files
6 (incl. references)
Skills in repo
3,342
Repo updated
First seen
Licence
MIT

At a glance

Troubleshoot Cursor codebase indexing: stuck indexing, empty search, @codebase failures, and performance issues.

  • Works in 3 steps: Reduce Scope → Resync Index → Clear Cache (if resync fails)
  • Cursor indexing
  • SKILL.md covers Overview, Prerequisites, Instructions and Output, plus 10 more sections
  • Calls cursor

What it does

Cursor Indexing Issues is an agent skill from jeremylongshore/tons-of-skills-marketplace. Troubleshoot Cursor codebase indexing: stuck indexing, empty search, @codebase failures, and performance issues. Triggers on "cursor indexing", "cursor index", "@codebase not working", "cursor search broken", "indexing stuck".

Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including reference files (for example `references/.cursorignore-configuration.md`, `references/common-indexing-issues.md` and `references/errors.md`). Compatibility notes: Designed for Claude Code

It sits in Development. The repository describes itself as: Model-agnostic agent-skills platform with a harness-free canonical layer, verified adapters, and the ccpi package manager. Explore at tonsofskills.com. The licence is MIT.

When your agent uses it

  • Cursor indexing
  • @codebase not working
  • Cursor search broken

Example prompts

  • “cursor indexing”
  • “cursor index”
  • “@codebase not working”
  • “/cursor-indexing-issues”

Requirements

  • Compatibility (from SKILL.md): Designed for Claude Code
  • Pre-approved tools (allowed-tools): Read, Write, Edit, Bash(cmd:*)

Workflow steps

3 steps, taken from the step headings in SKILL.md.

  1. Reduce Scope
  2. Resync Index
  3. Clear Cache (if resync fails)

What it can do on your machine

Read from SKILL.md and the folder at commit cfae287. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves these tools, so the agent can use them without asking each time:

    • Read
    • Write
    • Edit
    • Bash(cmd:*)

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • cursor

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • docs.cursor.com
    • cursor.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

  • Compatibility

    Designed for Claude Code

    From compatibility in the SKILL.md frontmatter.

Context cost

Cursor Indexing Issues loads about 2k tokens when it runs, and up to ~2.9k if it reads all its reference files. Until then it costs about 62 tokens; SKILL.md has 746 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~62
When it runs · the whole SKILL.md, loaded when a task matches
~2k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~2.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NoteMentions a .env fileSKILL.md:53
    chat to reference only that file. If a `.env` file becomes visible during testing, stop and correct the exclusion befor
  • NoteRuns commands with sudoSKILL.md:215
    o "fs.inotify.max_user_watches=524288" | sudo tee -a /etc/sysctl.conf
  • NoteRuns commands with sudoSKILL.md:216
    sudo sysctl -p

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from jeremylongshore/tons-of-skills-marketplace at commit cfae287, republished under its MIT licence (© jeremylongshore). 746 words, ~1,958 tokens.

Download SKILL.mdSave it as .claude/skills/cursor-indexing-issues/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.
name
cursor-indexing-issues
description
Troubleshoot Cursor codebase indexing: stuck indexing, empty search, @codebase failures, and performance issues. Triggers on "cursor indexing", "cursor index", "@codebase not working", "cursor search broken", "indexing stuck".
allowed-tools
Read, Write, Edit, Bash(cmd:*)
compatibility
Designed for Claude Code
version
1.19.0
license
MIT
author
Jeremy Longshore <jeremy@intentsolutions.io>
tags
saas, cursor, cursor-indexing

Cursor Indexing Issues

Overview

Diagnose missing, stale, slow, or over-broad codebase indexing while keeping sensitive and generated files excluded from AI context.

Prerequisites

  • The affected workspace, expected file/path, current ignore configuration, and a non-sensitive reproduction.
  • Authority to inspect repository indexing settings without weakening data-exclusion rules.

Instructions

  1. Confirm the file is inside an approved workspace root and not intentionally excluded by ignore configuration.
  2. Check index status, refresh only the affected workspace, and compare the result against a known expected file.
  3. Change ignore/rule configuration through normal review, then verify both inclusion of required files and exclusion of sensitive paths.

Output

  • A scoped indexing diagnosis with a verified inclusion/exclusion result.

Error Handling

ConditionSafe response
Sensitive file is indexedStop sharing context, add/repair the exclusion, and follow exposure policy.
Index remains staleCapture redacted diagnostics and escalate; do not remove all ignore controls.
Large repository is slowNarrow workspace roots and generated-file scope before resyncing.

Examples

When src/service.ts is absent, verify its root and ignore rules, resync indexing, then ask a minimal chat to reference only that file. If a .env file becomes visible during testing, stop and correct the exclusion before continuing.

Diagnose and fix codebase indexing problems. Covers stuck indexing, empty search results, stale results, and performance optimization for large codebases.

Quick Diagnosis

SymptomLikely CauseQuick Fix
Status bar stuck on "Indexing..."Large codebase or network issueAdd .cursorignore, resync
@Codebase returns nothingIndex not built or file excludedWait for index, check ignore files
@Codebase finds wrong codeStale indexResync index
Indexing crashes / restartsMemory or file watcher limitsIncrease limits, reduce scope
"Unable to index" errorNetwork blocked or auth expiredCheck proxy/firewall, re-auth

Fix: Stuck Indexing

Step 1: Reduce Scope

Create or update .cursorignore in project root:

gitignore
# .cursorignore -- exclude non-essential directories

# Build output
dist/
build/
.next/
out/
target/

# Dependencies (always exclude)
node_modules/
vendor/
.venv/
venv/

# Generated / large files
*.min.js
*.min.css
*.bundle.js
*.map
*.lock
package-lock.json
yarn.lock
pnpm-lock.yaml

# Data files
*.csv
*.sql
*.sqlite
*.parquet
*.json.gz
fixtures/

# Media
*.png
*.jpg
*.gif
*.svg
*.mp4
*.woff2
Step 2: Resync Index

Cmd+Shift+P > Cursor: Resync Index

Step 3: Clear Cache (if resync fails)
bash
# macOS
rm -rf ~/Library/Application\ Support/Cursor/Cache/
rm -rf ~/Library/Application\ Support/Cursor/CachedData/

# Linux
rm -rf ~/.config/Cursor/Cache/
rm -rf ~/.config/Cursor/CachedData/

# Windows (PowerShell)
Remove-Item -Recurse "$env:APPDATA\Cursor\Cache"
Remove-Item -Recurse "$env:APPDATA\Cursor\CachedData"

Restart Cursor after clearing cache. Full re-index begins automatically.

Fix: @Codebase Returns No Results

Check 1: Is Indexing Complete?

Look at the bottom status bar. If it says "Indexing...", wait for it to finish. For projects with 10K+ files, initial indexing can take 10-30 minutes.

Check 2: Is the File Excluded?

A file might be excluded by:

  1. .gitignore (Cursor respects this by default)
  2. .cursorignore (explicit exclusion)
  3. .cursorindexingignore (excluded from index but not from AI features)

Verify: Cursor Settings > Features > Codebase Indexing > View included files

This opens a text file listing all indexed paths. Search for the file you expect to find.

Check 3: Network Connectivity

Indexing requires network access to Cursor's embedding API. Test:

  • Can you access api.cursor.com?
  • Is a corporate proxy blocking outbound HTTPS?
  • Is a VPN interfering?
Show full SKILL.md (305 more words)Show less

@Codebase uses semantic search (embeddings), not keyword matching. The query "authentication middleware" will find files about auth even if they never use the word "middleware." But it may miss files if the semantic meaning is very different from the query.

For exact keyword matching, use Cmd+Shift+F (workspace search) instead.

Fix: Stale / Outdated Results

Cursor re-checks for file changes every 10 minutes using a Merkle tree. If you need fresher results:

  1. Save all open files
  2. Cmd+Shift+P > Cursor: Resync Index
  3. Wait for "Indexed" status to reappear
  4. Retry your @Codebase query

Performance Optimization for Large Projects

Indexing Time Benchmarks
Project SizeFiles IndexedInitial Index Time
Small (< 1K files)~500< 30 seconds
Medium (1K-10K files)~5,0001-5 minutes
Large (10K-50K files)~20,0005-30 minutes
Very large (50K+)~50,000+30 min - 2 hours
Monorepo Strategy

Do not open the entire monorepo root. Instead:

bash
# Open just the package you're working on:
cursor packages/api/

# Or use .cursorignore to exclude other packages:
# .cursorignore
packages/web/
packages/mobile/
packages/admin/
packages/deprecated-*
Linux File Watcher Limits

If indexing crashes on Linux with large projects:

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

# Increase to 524288 (persists across reboots)
echo "fs.inotify.max_user_watches=524288" | sudo tee -a /etc/sysctl.conf
sudo sysctl -p
Memory Pressure

If Cursor runs out of memory during indexing:

json
// settings.json
{
  "files.maxMemoryForLargeFilesMB": 4096,
  "files.watcherExclude": {
    "**/node_modules/**": true,
    "**/.git/**": true,
    "**/dist/**": true,
    "**/build/**": true
  }
}

.cursorignore vs .cursorindexingignore

FileIndexed?Available to AI?Use Case
Listed in .cursorignoreNoNo (best effort)Secrets, large binaries, build output
Listed in .cursorindexingignoreNoYes (via @Files)Test fixtures, docs, large but useful files
Not in any ignore fileYesYesYour source code

Use .cursorindexingignore for files you want to reference explicitly but not have polluting search results:

gitignore
# .cursorindexingignore
tests/fixtures/large-sample.json
docs/api-spec.yaml
e2e/recordings/

Enterprise Considerations

  • Data residency: Embeddings stored in Turbopuffer cloud. No plaintext code stored, but metadata (obfuscated filenames) exists server-side
  • Air-gapped environments: Indexing requires outbound HTTPS. Not available in fully air-gapped setups
  • Index freshness SLA: 10-minute polling interval is not configurable. Manual resync is the only way to force immediate re-index
  • Audit: No logging of which files are indexed. Use .cursorignore proactively for regulated data

Resources

© jeremylongshore, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 5 other files (references) in skills/.curated/cursor-indexing-issues of jeremylongshore/tons-of-skills-marketplace.

  • SKILL.md
  • references/.cursorignore-configuration.md
  • references/common-indexing-issues.md
  • references/errors.md
  • references/examples.md
  • references/index-verification.md

Open the folder on GitHubat commit cfae287

Compare with similar skills

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PR Babysitteropeninterpreter/openinterpreter69k3 repos~4.2kAutomated safety check: PassApache-2.0
Code Review ChecklistshareAI-lab/learn-claude-code78k4 repos~1.1kAutomated safety check: PassMIT

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Categories

Questions about Cursor Indexing Issues

What does Cursor Indexing Issues do?

Troubleshoot Cursor codebase indexing: stuck indexing, empty search, @codebase failures, and performance issues. Cursor Indexing Issues is an agent skill from jeremylongshore/tons-of-skills-marketplace. Troubleshoot Cursor codebase indexing: stuck indexing, empty search, @codebase failures, and performance issues.

When should I use Cursor Indexing Issues?

Cursor Indexing Issues fits situations like: Cursor indexing; @codebase not working; Cursor search broken.

How do I install Cursor Indexing Issues in Claude Code?

Run `npx skills add jeremylongshore/tons-of-skills-marketplace --skill cursor-indexing-issues -a claude-code`. Or copy the skill folder (skills/.curated/cursor-indexing-issues in jeremylongshore/tons-of-skills-marketplace) into .claude/skills/cursor-indexing-issues in your project. Claude Code loads it when a task matches its description.

How do I install Cursor Indexing Issues in Codex?

Run `npx skills add jeremylongshore/tons-of-skills-marketplace --skill cursor-indexing-issues -a codex`. Or copy the skill folder (skills/.curated/cursor-indexing-issues in jeremylongshore/tons-of-skills-marketplace) into .agents/skills/cursor-indexing-issues in your project. Codex loads it when a task matches its description.

Can I use Cursor Indexing Issues in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add jeremylongshore/tons-of-skills-marketplace --skill cursor-indexing-issues -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/cursor-indexing-issues, .gemini/skills/cursor-indexing-issues, .github/skills/cursor-indexing-issues and .opencode/skills/cursor-indexing-issues in your project.

What does Cursor Indexing Issues need to run?

Going by SKILL.md and its folder, Cursor Indexing Issues needs the command-line tools its instructions call (cursor). Its frontmatter pre-approves these tools: Read, Write, Edit, Bash(cmd:*). Compatibility (from SKILL.md): Designed for Claude Code.

Does Cursor Indexing Issues access the network?

SKILL.md names 2 domains. As links in the text: docs.cursor.com and cursor.com. This is read from the text; nothing was executed.

Is Cursor Indexing Issues safe to install?

Our automated static check of SKILL.md found notes only (mentions a .env file; runs commands with sudo), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Cursor Indexing Issues use?

Cursor Indexing Issues is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Cursor Indexing Issues use?

About 2k tokens (SKILL.md is roughly 7.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 956 tokens, read only when the agent opens those files.

What are the alternatives to Cursor Indexing Issues?

Skills that share tags, products or a category with Cursor Indexing Issues: Vercel Composition Patterns (supabase/supabase, 111k stars), Finishing a Development Branch (obra/superpowers, 297k stars), Typescript Advanced Types (rolling-scopes/rsschool-app, 10k stars) and PR Babysitter (openinterpreter/openinterpreter, 69k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Cursor Indexing Issues?

jeremylongshore (a GitHub user) maintains it in jeremylongshore/tons-of-skills-marketplace, which has 2,827 GitHub stars. The repository holds 3,342 skills in this directory. The repository was last updated on October 10, 2026.

Source: jeremylongshore/tons-of-skills-marketplace on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.