False positive diagnostic warning: PATH contains ~/.local/bin but system shows it as missing

Bug Report

Description

The system diagnostic shows a false positive warning about ~/.local/bin not being in PATH, even though it is correctly configured and working.

Diagnostic Message

⚠ Native installation exists but ~/.local/bin is not in your PATH. Run:
  echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.zshrc && source ~/.zshrc

Environment

• OS: macOS (Darwin)
• Claude Code Version: 2.1.19 (also tested on 2.1.17)
• Shell: zsh with Oh My Zsh
• Installation Method: Native installation

Verification Steps

1. .zshrc Configuration (Line 8):

``bash
export PATH="$HOME/.local/bin:$PATH"
``

1. Current PATH Verification:

``bash
echo $PATH
# Output includes: /Users/ip9202/.local/bin
``

1. Binary Verification:

```bash
which claude
# Output: /Users/ip9202/.local/bin/claude

claude --version
# Output: 2.1.19 (Claude Code)
```

1. Symlink Verification:

``bash
ls -la ~/.local/bin/claude
# Output: lrwxr-xr-x@ 1 ip9202 staff 49 -> /Users/ip9202/.local/share/claude/versions/2.1.19
``

Expected Behavior

No diagnostic warning should be shown since ~/.local/bin is correctly in PATH and the claude command works normally.

Actual Behavior

The diagnostic warning persistsently appears on every session start, even though:

• PATH is correctly configured in .zshrc
• Current session PATH includes ~/.local/bin
• claude command executes successfully
• Symlink is properly set up

Impact

• Low functional impact (everything works correctly)
• High noise impact (false positive warning on every session)
• User confusion about installation status

Timeline

• This issue appeared after automatic update to version 2.1.19 (installed 2025-01-24 08:37)
• Previous version (earlier today) worked without this warning
• Downgrading to 2.1.17 did not resolve the issue

Hypothesis

The diagnostic check logic may be:

1. Checking PATH in an isolated environment without sourcing .zshrc
2. Using a different method to verify PATH than the actual shell session
3. Caching old diagnostic results
4. Checking for a specific PATH format rather than actual availability

Additional Context

The issue suggests that the system diagnostic runs in a different environment than the actual shell session, or there's a bug in how PATH is verified.

---

Environment Details:

# PATH output
echo $PATH
/Users/ip9202/.local/bin:/opt/homebrew/bin:...[truncated]

# .zshrc status
ls -la ~/.zshrc
-rw-r--r--@ 1 ip9202 staff 4449 Jan 24 14:11 /Users/ip9202/.zshrc

# Claude binary
file ~/.local/bin/claude
/Users/ip9202/.local/bin/claude: Mach-O 64-bit executable arm64