[BUG] `installMethod` config setting ignored when `~/.local/bin/` exists

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

When Claude Code is installed system-wide (e.g., /usr/local/bin/claude) and I set "installMethod": "system" in ~/.claude.json, Claude Code ignores this setting and displays a warning about native installation.

The warning appears in the Claude Code UI status bar whenever ~/.local/bin/ directory exists (even for unrelated purposes like pipx or user scripts) and there is no ~/.local/bin/claude file.

What Should Happen?

Claude Code should respect the installMethod setting in ~/.claude.json. When explicitly set to "system", it should not check for native installation paths or display native installation warnings.

Error Messages/Logs

installMethod is native, but claude command not found at /home/user/.local/bin/claude


This message appears in the UI status bar despite `~/.claude.json` containing:

{
  "installMethod": "system",
  ...
}

Steps to Reproduce

1. Have Claude Code installed system-wide:

``bash
which claude
# Output: /usr/local/bin/claude
``

1. Authenticate with Claude (creates ~/.claude.json):

``bash
claude
``

1. Set installMethod to "system" in config:

``bash
jq '.installMethod = "system"' ~/.claude.json > /tmp/c.json && mv /tmp/c.json ~/.claude.json
``

1. Verify the config is correct:

``bash
jq '.installMethod' ~/.claude.json
# Output: "system"
``

1. Create ~/.local/bin/ for some other purpose (e.g., pipx, user scripts):

``bash
mkdir -p ~/.local/bin
touch ~/.local/bin/my-other-tool
``

1. Launch Claude Code:

``bash
claude
``

1. Bug: Warning appears in UI despite installMethod=system:

``
installMethod is native, but claude command not found at /home/user/.local/bin/claude
``

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.3 (Claude Code)

Platform

Other

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

Root cause analysis:

Claude Code appears to have two independent checks:

1. Config-based: Reads installMethod from ~/.claude.json
2. Detection-based: Scans for ~/.local/bin/ directory existence

The detection-based check overrides the config setting. When it detects ~/.local/bin/ exists, it assumes a native installation was intended and checks for ~/.local/bin/claude, ignoring the explicit "installMethod": "system" setting.

Workaround:

Create a symlink to satisfy the detection:

ln -sf /usr/local/bin/claude ~/.local/bin/claude

Suggested fix:

When installMethod is explicitly set to "system" in ~/.claude.json:

• Skip native installation path detection
• Don't check for ~/.local/bin/claude
• Don't display native installation warnings

The config setting should be authoritative when explicitly set by the user.