[BUG] Multiple installation conflicts still occurring (v2.0.26) - npm-local + native binary

[memorymuse]

Preflight Checklist

• I have searched existing issues and this hasn't been reported yet
• This is a single bug report
• I am using the latest version of Claude Code

What's Wrong?

Multiple installation conflicts between npm-local and native binary installations persist in v2.0.26, despite #7734 being closed on 9/24/2025 with the note "This should be resolved in the next release".

Symptoms:

• claude command fails with "No such file or directory"
• Diagnostics show "Multiple installations found" warnings
• Config file (~/.claude.json) reverts to "installMethod": "local" after restarts
• Shell wrappers/aliases continue pointing to deleted npm-local paths

What Should Happen?

After removing npm-local installation and switching to native binary:

1. Diagnostics should show single installation
2. Config should persist as "installMethod": "native" across restarts
3. Shell should resolve to native binary without errors

Error Messages/Logs

$ claude --version
-bash: /home/username/.claude/local/claude: No such file or directory

$ # After initial fix attempt:
$ claude /diagnostics

 Diagnostics
 └ Currently running: native (2.0.26)
 └ Path: /home/username/.local/bin/claude
 └ Invoked: /home/username/.local/share/claude/versions/2.0.26
 └ Config install method: local
 └ Auto-updates enabled: false
 └ Search: OK (bundled)
 Warning: Multiple installations found
 └ npm-local at /home/username/.claude/local
 └ native at /home/username/.local/bin/claude
 Warning: Running native installation but config install method is 'local'
 Fix: Run claude install to update configuration
 Warning: Leftover npm local installation at /home/username/.claude/local
 Fix: Run: rm -rf /home/username/.claude/local

Steps to Reproduce

1. Have npm-local installation at ~/.claude/local/
2. Install native binary via curl -fsSL https://claude.ai/install.sh | bash
3. Remove ~/.claude/local/ directory
4. Edit ~/.claude.json to set "installMethod": "native"
5. Restart Claude Code → works fine
6. Exit and restart again → warnings return, config reverted to "local"

Expected: Config stays "native", no warnings
Actual: Config reverts, ~/.claude/local sometimes recreated

Claude Model

Sonnet 4.5 (claude-sonnet-4-5-20250929)

Is this a regression?

Yes - #7734 was closed as "will be fixed in next release" but issue persists

Last Working Version

N/A - migrating from npm-local to native

Claude Code Version

2.0.26 (Claude Code)

Platform

WSL2

Operating System

Linux (Ubuntu on WSL2)

Terminal/Shell

bash

Additional Information

Environment:

• NVM with multiple Node versions installed
• Previous npm-global installations across multiple Node versions (nvm isolation)
• Shell wrappers/aliases from old installation methods

Related Issues:

• [BUG] npm install may conflict with native install #7734 (closed, claimed fixed)
• Windows – install method keeps flipping (unknown ↔︎ npm-global) despite native install; want stable native setup #5540 (install method flipping on Windows)
• [BUG] False positive "Config mismatch" warning when installation method matches #7231 (false positive config mismatch)
• [BUG] : fresh native installation raise warning about npm #9666 (fresh native install warns about npm)

Root cause appears to be:

1. Stale shell state (aliases, functions, hash cache)
2. Zombie Claude processes from other terminals
3. Config file being reverted by running processes
4. Shell wrappers pointing to old paths

[github-actions]

Found 3 possible duplicate issues:

1. [BUG] npm install may conflict with native install #7734
2. [BUG] : fresh native installation raise warning about npm #9666
3. Windows – install method keeps flipping (unknown ↔︎ npm-global) despite native install; want stable native setup #5540

This issue will be automatically closed as a duplicate in 3 days.

• If your issue is a duplicate, please close it and 👍 the existing issue instead
• To prevent auto-closure, add a comment or 👎 this comment

🤖 Generated with Claude Code

[memorymuse]

Working Fix (Tested on WSL2 + NVM)

This fix installs/uses the native binary version (not npm-based). It does NOT remove your settings, history, or other .claude/ files - only the conflicting npm-local installation.

Successfully resolves: "No such file or directory" errors, diagnostics warnings, config reverting to "local" after restarts.

---

Solution (5 Steps)

1. Remove npm-local installation

rm -rf ~/.claude/local
# Verify: ls ~/.claude/local → should error

2. Fix config file

# Edit ~/.claude.json - change this line:
# "installMethod": "local" → "installMethod": "native"

grep installMethod ~/.claude.json  # Should show: "installMethod": "native"

3. Remove shell wrappers/aliases

# Edit ~/.bashrc (or ~/.zshrc) and remove any:
#   - alias claude="..."
#   - claude() { ... } functions  
#   - Auto-update scripts

source ~/.bashrc

# Verify:
type claude  # Should show PATH only, NOT "aliased to" or "is a function"

4. Clear shell cache

unalias claude 2>/dev/null && hash -r  # bash
# zsh users: use 'rehash' instead of 'hash -r'

which claude  # Should show: /home/username/.local/bin/claude

5. Kill zombie Claude sessions

# Exit ALL other Claude Code terminal windows/tabs
ps aux | grep '[c]laude'  # Should see minimal processes after cleanup

---

Verify Fix (Critical!)

Test persistence across restarts:

1. Exit Claude Code completely
2. Restart Claude Code → send any message (creates session log)
3. Exit again
4. Restart again → check for diagnostics warnings

✅ Success = No warnings on the 2nd restart

If warnings return, the config is reverting - see troubleshooting below.

---

Troubleshooting

Config keeps reverting to "local"

• Zombie processes still running:

  ps aux | grep '[c]laude'  # Kill old PIDs

• Multiple terminal sessions: Close ALL terminals, open fresh window

"No such file or directory" persists

• Open new terminal WINDOW (not just a new tab)
• Check: type claude - if shows alias/function, repeat step 3

~/.claude/local keeps recreating

• Check ~/.bashrc or ~/.zshrc for auto-update scripts calling npm install
• Check ~/.bashrc.bak - old configs might be sourced accidentally

NVM users - multiple global installs across Node versions

# Check for installations across all Node versions:
find ~/.nvm -name "*claude*"

# Remove from ALL Node versions:
for v in ~/.nvm/versions/node/*/; do 
  npm uninstall -g @anthropic-ai/claude-code --prefix="$v"
done

Why this happens: NVM isolates global packages per Node version. Installing Claude in Node 18, then switching to Node 20 and reinstalling creates duplicate global installations.

WSL: npm/node showing Windows paths (/mnt/c/...)

which npm node
# If seeing /mnt/c/ paths:
npm config set prefix ~/.npm-global
export PATH="$HOME/.npm-global/bin:$PATH"  # Add to ~/.bashrc to persist

Nuclear option (last resort)

# Backup your work first!
rm -rf ~/.claude/local ~/.local/share/claude ~/.local/bin/claude
curl -fsSL https://claude.ai/install.sh | bash

---

Important: Shell sessions cache commands aggressively. After making changes, always test in a fresh terminal window to confirm the fix persists.

---

Tested on WSL2 + NVM environment with multiple Node versions. Hope this helps!

[github-actions]

This issue has been automatically locked since it was closed and has not had any activity for 7 days. If you're experiencing a similar issue, please file a new issue and reference this one if it's relevant.