[BUG] claude code can't access external projects if running via sandboxed environment

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

When using Visual Code with the Claude code extension, if we open a project under /run/media/system/<device>/project.

and then ask claude to do a simple whoami:

``Exit code 1
Portal call failed: Failed to start command: Failed to execute child process ?source /home/user/.claude/shell-snapshots/snapshot-bash-1777392203949-xdap7g.sh 2>/dev/null || true && { shopt -u extglob || setopt NO_EXTENDED_GLOB; } >/dev/null 2>&1 || true && eval whoami < /dev/null && pwd -P >| /tmp/claude-7620-cwd? (No such file or directory)``.

What Should Happen?

It should return the username such as: whoami -> user.

Error Messages/Logs

code 1
Portal call failed: Failed to start command: Failed to execute child process ?source /home/user/.claude/shell-snapshots/snapshot-bash-1777392203949-xdap7g.sh 2>/dev/null || true && { shopt -u extglob || setopt NO_EXTENDED_GLOB; } >/dev/null 2>&1 || true && eval whoami < /dev/null && pwd -P >| /tmp/claude-7620-cwd? (No such file or directory).

Steps to Reproduce

1. have flatpak version of visual code installed (the same problem emerge if installed via distrobox too)
2. open a project that isn't in the root partition, under /run/media/system/<device>/<project>
3. ask claude to run whoami
4. it should complain that it can't find said file or directory.

Claude Model

Not sure / Multiple models

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

v2.1.121

Platform

Anthropic API

Operating System

Other Linux

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_