[BUG] Claude Code Not Inheriting Environment Variables like PATH, PYTHONPATH from Shell or settings.json

Environment

• Platform (select one):
• [ ] Anthropic API
• [X] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.69
• Operating System: Ubuntu 22.04.1
• Terminal: iTerm2
• Shell: zsh

Bug Description

In my shell, the environment variables PATH and PYTHONPATH have the following values:

• PATH: /home/coder/.local/share/tmp/some-bazel-env/bin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/coder/.local/bin
• PYTHONPATH: /home/coder/.local/share/tmp/some-other-bazel-env/bin

I also added these to the current working directory's .claude/settings.json:

{
    "env": {
        "PATH": "/home/coder/.local/share/tmp/some-bazel-env/bin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/coder/.local/bin",
        "PYTHONPATH": "/home/coder/.local/share/tmp/some-other-bazel-env/bin"
   }
}

When I open claude, it shows different env vars from the ones above.

Steps to Reproduce

1. Set env vars in the shell via export PATH=/home/coder/.local/share/tmp/some-bazel-env/bin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/coder/.local/bin and export PYTHONPATH=/home/coder/.local/share/tmp/some-other-bazel-env/bin.
2. Open claude
3. ! echo $PATH and ! echo $PYTHONPATH

Expected Behavior

I should see ! echo $PATH return /home/coder/.local/share/tmp/some-bazel-env/bin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/coder/.local/bin exactly and ! echo $PYTHONPATH return /home/coder/.local/share/tmp/some-other-bazel-env/bin exactly.

Actual Behavior

I see other paths being prepended to PATH and PYTHONPATH, affecting the ordering of executables.

For example, ! echo $PATH shows /some-other-path-1:/some-other-path-2:/home/coder/.local/share/tmp/some-bazel-env/bin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/coder/.local/bin

Additional Context

N/A