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

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report
• [x] 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:

• #7734 (closed, claimed fixed)
• #5540 (install method flipping on Windows)
• #7231 (false positive config mismatch)
• #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