Sandbox creates phantom dotfiles in project directory instead of protecting home directory files

Description

When Claude Code's sandbox initializes, it creates empty (0-byte), read-only placeholder files in the current working directory for various dotfiles that should only be protected in $HOME. These phantom files persist after the session ends and clutter the project directory.

Affected files created in CWD

• .bash_profile
• .bashrc
• .gitconfig
• .gitmodules
• .idea
• .mcp.json
• .profile
• .ripgreprc
• .vscode
• .zprofile
• .zshrc

Evidence

The bwrap command shows incorrect --ro-bind entries that bind from/to the project directory:

--ro-bind /home/user/project/.bashrc /home/user/project/.bashrc
--ro-bind /home/user/project/.zshrc /home/user/project/.zshrc
--ro-bind /home/user/project/.gitconfig /home/user/project/.gitconfig
(etc.)

These should presumably be protecting ~/.bashrc, ~/.zshrc, etc. in the home directory, not creating files in the project.

File characteristics

$ ls -la .bashrc
-r--r--r-- 1 user user 0 Jan  9 21:03 .bashrc

$ file .bashrc
.bashrc: empty

• All files are 0 bytes
• All are read-only (0444 permissions)
• All share the same creation timestamp (sandbox init time)
• Cannot be deleted from within the sandbox

Expected behavior

The sandbox should protect sensitive dotfiles in $HOME without creating any files in the project directory.

Actual behavior

Empty placeholder files are created in the project directory as bind mount targets.

Environment

• OS: Linux (Arch Linux 6.18.3)
• Claude Code version: latest as of 2025-01-09
• Shell: bash/zsh
• Dotfile manager: chezmoi (may be related - these are the files chezmoi tracks in $HOME)

Workaround

Manually delete the files after exiting Claude Code:

rm -f .bash_profile .bashrc .gitconfig .gitmodules .idea .mcp.json .profile .ripgreprc .vscode .zprofile .zshrc