[BUG] Shell initialization (cd ~ in .bashrc) breaks workspace boundary

Description

Claude Code's Bash tool executes commands outside the intended workspace when user's .bashrc or .zshrc contains directory change commands (e.g., cd ~).

Root Cause

When the Bash tool starts its persistent shell session, it sources the user's shell configuration file (.bashrc, .zshrc, etc.). If this configuration contains commands that change the working directory (like cd ~), the shell starts in the wrong directory despite Claude Code's working directory being set correctly.

Reproduction Steps

1. Add cd ~ to the top of your ~/.bashrc file
2. Start Claude Code in a project directory: /home/user/my-project/
3. Run any Bash command via CC that uses relative paths (e.g., find . -name "*.md")
4. Observe that the command executes from /home/user/ instead of /home/user/my-project/

Expected Behavior

Bash commands should execute within the workspace directory regardless of shell initialization scripts.

Actual Behavior

• First Bash command executes from wrong directory (e.g., home directory)
• System then resets cwd with message: "Shell cwd was reset to /home/user/my-project/"
• This causes CC to search/modify files outside the intended workspace
• Violates the fundamental workspace boundary principle

Impact

• Security concern: CC can inadvertently access/modify files outside workspace
• Data corruption risk: Commands like find or file operations may affect wrong directories
• Confusing behavior: Users expect CC to operate only within workspace
• Related to existing issues: #5038, #11067, #7442, #3275

Current Workaround

Remove directory-changing commands from shell initialization files.

Suggested Solutions

1. Start Bash in workspace directory explicitly: After sourcing shell config, force cd to workspace directory
2. Sandbox shell initialization: Source a minimal environment instead of full user config
3. Detect and warn: Check if cwd changed after sourcing config and warn user
4. Document best practices: Add warning in docs about shell config affecting workspace boundaries

Environment

• OS: Ubuntu Linux (WSL2)
• Shell: bash
• Claude Code version: Latest (as of December 2024)
• Configuration: cd ~ at line 1 of ~/.bashrc

Additional Context

This is a subtle issue that many users might not notice until CC starts operating outside their workspace. The "Shell cwd was reset" message indicates the system detects this, but it happens after the command executes in the wrong directory.

Users coming from various shell configurations (especially those with custom workspace management) may unknowingly have this problem without understanding why CC behaves unexpectedly.