still borks for nightly upgrades

[acoliver]

What happened?

npm i -g @vybestack/llxprt-code@nightly
npm error code ENOTEMPTY
npm error syscall rename
npm error path /opt/homebrew/lib/node_modules/@vybestack/llxprt-code
npm error dest /opt/homebrew/lib/node_modules/@vybestack/.llxprt-code-ofqtIqCy
npm error errno -66
npm error ENOTEMPTY: directory not empty, rename '/opt/homebrew/lib/node_modules/@vybestack/llxprt-code' -> '/opt/homebrew/lib/node_modules/@vybestack/.llxprt-code-ofqtIqCy'
npm error A complete log of this run can be found in: /Users/acoliver/.npm/_logs/2026-01-17T13_36_20_032Z-debug-0.log

this happens virtually every time.

What did you expect to happen?

not do that. I can recover by deleting that directory but then it still doesn't set the execute permissions on /opt/homebrew/lib/node_modules/@vybestack/llxprt-code/dist/index.js so it still borks. We tried to fix this before but it still sint' fixed.

Client information

About LLxprt Code

CLI Version 0.8.0-nightly.260117.e51b99d94
Git Commit af84cd4
Model openai:hf:zai-org/GLM-4.7
Provider openai
Base URL https://api.synthetic.new/openai/v1
Sandbox no sandbox
OS darwin
Auth Method provider

Login information

No response

Anything else we need to know?

No response

[acoliver]

@CodeRabbit can you look into this?

[coderabbitai]

📝 CodeRabbit Plan Mode

Generate an implementation plan and prompts that you can use with your favorite coding agent.

• Create Plan

Examples

• Example 1
• Example 2

---

⚠️ Possible Duplicate Issue

• most upgrades bork #1137

🔗 Related PRs

#1141 - fix(auto-update): prevent ENOTEMPTY errors with atomic locking [merged]

---

🧪 Issue enrichment is currently in open beta.

You can configure auto-planning by selecting labels in the issue_enrichment configuration.

To disable automatic issue enrichment, add the following to your .coderabbit.yaml:

issue_enrichment:
  auto_enrich:
    enabled: false

💬 Have feedback or questions? Drop into our discord!

[coderabbitai]

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Fetch the details of issue `#1162`
gh issue view 1162 --repo vybestack/llxprt-code --json title,body,author,labels,assignees,state,comments

Length of output: 2293

---

🏁 Script executed:

#!/bin/bash
# Find and read the package.json file
fd -t f "^package.json$" --max-depth 2 -x cat {}

Length of output: 6271

---

🏁 Script executed:

#!/bin/bash
# Read the postinstall script
echo "=== postinstall.cjs ==="
cat scripts/postinstall.cjs

echo -e "\n=== prepare-package.js ==="
cat scripts/prepare-package.js

# Check if dist directory exists
echo -e "\n=== Checking for dist directory ==="
fd -t d "^dist$" --max-depth 3

# Search for previous issues/PRs mentioning this problem
echo -e "\n=== Searching for related issues ==="
gh search issues --repo vybestack/llxprt-code "ENOTEMPTY OR execute permissions OR nightly upgrade" --limit 10 --json number,title,state

# Search for recent PRs that might have attempted to fix this
echo -e "\n=== Searching for related PRs ==="
gh search prs --repo vybestack/llxprt-code "postinstall OR permissions OR bin OR ENOTEMPTY" --limit 10 --json number,title,state,mergedAt

Length of output: 5351

---

🏁 Script executed:

#!/bin/bash
# Check the version script for nightly build process
echo "=== version.js ==="
cat scripts/version.js

# Look for bundle/llxprt.js to see if it has proper shebang
echo -e "\n=== Checking bundle/llxprt.js (if exists) ==="
if [ -f bundle/llxprt.js ]; then
  head -n 5 bundle/llxprt.js
else
  echo "bundle/llxprt.js not found"
fi

# Search for any references to chmod or permissions in the codebase
echo -e "\n=== Searching for chmod/permissions handling ==="
rg -n "chmod|0o755|executable|permissions" scripts/ --type js -C 2

# Search for ENOTEMPTY or npm install issues in code
echo -e "\n=== Searching for ENOTEMPTY or install issues ==="
rg -n "ENOTEMPTY|npm.*install|postinstall" scripts/ --type js -C 2

# Check the bundle creation script
echo -e "\n=== esbuild.config.js ==="
cat esbuild.config.js

# Check copy bundle assets script
echo -e "\n=== copy_bundle_assets.js ==="
cat scripts/copy_bundle_assets.js

Length of output: 24012

---

🏁 Script executed:

#!/bin/bash
# Search for previous issues/PRs about permissions or install problems
gh search issues --repo vybestack/llxprt-code "permissions OR chmod OR execute OR bin" --limit 15 --json number,title,state,body --jq '.[] | "\(.number): \(.title) [\(.state)]"'

# Search commit history for fixes related to this
git log --all --oneline --grep="permission\|chmod\|postinstall\|ENOTEMPTY" -20

# Check if there's a .npmignore or files configuration that might affect what gets published
echo -e "\n=== Checking for .npmignore ==="
cat .npmignore 2>/dev/null || echo "No .npmignore found"

# Check the actual bin entry point file to see if it has a shebang
echo -e "\n=== Checking CLI entry point ==="
head -n 10 packages/cli/index.ts

# Search for any GitHub Actions or CI scripts that handle publishing
echo -e "\n=== Searching for publish/release workflows ==="
fd -t f "publish|release" .github/workflows/ -x cat {}

Length of output: 25083

---

🏁 Script executed:

#!/bin/bash
# Check if npm pack preserves the execute permissions set by chmod
echo "=== Verifying file permissions in package ==="

# Simulate what happens during npm publish by running npm pack
npm run bundle 2>&1 | tail -n 5

# Check if bundle/llxprt.js exists and has execute permissions
if [ -f bundle/llxprt.js ]; then
  echo "bundle/llxprt.js permissions:"
  ls -la bundle/llxprt.js
  
  # Create a test pack to see what npm pack does with permissions
  echo -e "\n=== Creating test package ==="
  npm pack --dry-run 2>&1 | head -n 20
  
  # Check what files would be included
  echo -e "\n=== Files that would be included in package ==="
  npm pack --dry-run 2>&1 | grep -E "bundle/|scripts/postinstall"
else
  echo "bundle/llxprt.js does not exist, would need to run build first"
fi

# Check if there's any preuninstall or cleanup scripts
echo -e "\n=== Checking for uninstall hooks ==="
rg -n "preuninstall|uninstall|cleanup" package.json

# Look for any migration or version check logic
echo -e "\n=== Checking for migration logic ==="
rg -n "migration|upgrade|version.*check" scripts/postinstall.cjs

Length of output: 295

---

🏁 Script executed:

#!/bin/bash
# Search git history for when the package structure changed from dist/ to bundle/
echo "=== Searching for package structure changes ==="
git log --all --oneline --grep="dist\|bundle" -20

echo -e "\n=== Searching for changes to bin field in package.json ==="
git log --all -p --follow -S"\"bin\"" -- package.json | head -n 100

echo -e "\n=== Checking if there's a preuninstall or cleanup issue/PR ==="
gh search issues --repo vybestack/llxprt-code "preuninstall OR cleanup OR uninstall" --limit 5 --json number,title,state

# Look for the auto-update fix mentioned in commit log
echo -e "\n=== Examining the previous ENOTEMPTY fix (commit 928704b6) ==="
git show --stat 928704b6 2>/dev/null || echo "Commit not available in current branch"

# Check if npm handles executable permissions automatically via bin field
echo -e "\n=== Checking bin field configuration ==="
cat package.json | jq '.bin'

# Look for issues or discussions about global install problems
echo -e "\n=== Searching for global install issues ==="
gh search issues --repo vybestack/llxprt-code "global install OR npm install -g" --limit 10 --json number,title,state,body --jq '.[] | "\(.number): \(.title) [\(.state)]"'

Length of output: 8099

---

🏁 Script executed:

#!/bin/bash
# Find when the bin field changed from dist/ to bundle/
echo "=== Finding when package structure changed from dist to bundle ==="
git log --all --oneline -S"dist/index.js" -- package.json | head -n 10

# Check if there are any .npmignore rules that might affect this
echo -e "\n=== Checking for any npm ignore patterns ==="
cat .npmignore 2>/dev/null || echo "No .npmignore file"

# Look at the files array more closely
echo -e "\n=== Current files configuration ==="
cat package.json | jq '.files'

# Check what npm would actually pack
echo -e "\n=== Simulating npm pack to see what files would be included ==="
# Create a minimal check without actually building
npm pkg get files bin

# Look for any historical issues about package structure
echo -e "\n=== Looking for issues about package upgrade or structure ==="
gh search issues --repo vybestack/llxprt-code "upgrade OR structure OR rename" --state all --limit 5 --json number,title,state

# Check the postinstall script more carefully for any cleanup logic
echo -e "\n=== Re-examining postinstall for cleanup opportunities ==="
cat scripts/postinstall.cjs | grep -A 10 -B 10 "bundle\|dist" || echo "No bundle/dist references in postinstall"

# Look at what Homebrew npm global installs look like and if they're special-cased
echo -e "\n=== Checking for Homebrew-specific handling ==="
rg -n "homebrew|/opt/homebrew" packages/ -t ts -C 2

Length of output: 9238

---

@acoliver, I've investigated this issue and found the root cause. The problem is a package structure migration issue combined with npm's inability to handle the atomic rename during global package upgrades.

Root Cause

Your system has an old installation that used the dist/index.js structure, but the current package uses bundle/llxprt.js. When npm tries to upgrade, it encounters:

1. ENOTEMPTY error: npm attempts to atomically rename /opt/homebrew/lib/node_modules/@vybestack/llxprt-code but can't because the old dist/ directory structure conflicts with the new bundle/ structure
2. Permission issue: You're seeing references to dist/index.js which confirms you have a stale installation - the current package doesn't even use that path anymore

The previous ENOTEMPTY fix in commit 928704b6 addressed concurrent auto-updates, but not this package structure migration scenario.

Immediate Workaround

# Complete uninstall (with force to handle broken state)
npm uninstall -g `@vybestack/llxprt-code`
# Manually clean up any leftover directories
rm -rf /opt/homebrew/lib/node_modules/@vybestack/llxprt-code
rm -rf /opt/homebrew/lib/node_modules/@vybestack/.llxprt-code-*

# Fresh install
npm install -g `@vybestack/llxprt-code`@nightly

Long-term Fix Needed

The codebase needs a preuninstall script to handle cleanup during package upgrades. Currently there's only a postinstall.cjs that handles GitHub installations. I recommend:

1. Add a preuninstall script (scripts/preuninstall.cjs) that:

   • Detects old dist/ directory structure
   • Cleans it up before npm attempts the rename
   • Handles leftover .llxprt-code-* temp directories

2. Update package.json to include:

   "scripts": {
     "preuninstall": "node scripts/preuninstall.cjs"
   }

Would you like me to create an issue for this, or would you prefer I plan the code changes to implement the preuninstall script?