[BUG] Claude Edits Shell RC file on startup

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.81
• Operating System: Ubuntu 24.04
• Terminal: Terminal

Bug Description

I had a custom node_modules location aliased in my shell's RC file, upon starting claude, it would remove that alias entirely, not replacing it with anything.

Running claude migrate-installer did the "right" thing and installed it in ~/.local/claude, and then edited that alias into my RC file, but it's a little concerning that the process is editing anything outside of the local directory without being explicit about it. It's a little concerning that an AI tool would edit anything that I'm not explicitly allowing it to.

Steps to Reproduce

1. Install claude in non-standard location using npm install
2. Set alias in shell's RC file to that nonstandard location
3. Run claude - see that custom alias has been removed from RC file.

Expected Behavior

Claude not editing a file outside of the directory it is running in or any local caches it uses.

Actual Behavior

Claude removes custom Alias

Additional Context

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