[BUG] Bash tool silently drops stdout from node processes when script path is under ~/.claude/

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?

Bash tool silently drops stdout from node processes when the script path resolves under ~/.claude/. The process exits 0, no errors on stderr - output is just gone.

This breaks custom skills that shell out to node scripts when ~/.claude/skills/ is a symlink to an external directory.

Repro

1. Have a node script that makes HTTP requests and writes JSON to stdout (e.g. a task management CLI client).
2. Place it under ~/.config/mytools/skills/myscript/scripts/client.mjs.
3. Symlink: ln -s ~/.config/mytools/skills ~/.claude/skills
4. The skill's shell wrapper uses SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)" which resolves to the logical (symlink) path under ~/.claude/.

Via ~/.claude/ path - no output:

# From Claude Code Bash tool:
printf '%s' "some-input" | node ~/.claude/skills/myscript/scripts/client.mjs list
# Result: empty stdout, exit 0

Via resolved path - works:

# Same script, same node binary, same args:
printf '%s' "some-input" | node ~/.config/mytools/skills/myscript/scripts/client.mjs list
# Result: full JSON output

Key observations

• Files are identical (diff returns 0) - one is accessed through the symlink, the other directly
• Same node binary, same stdin input, same arguments
• .claude/ path: empty stdout, empty stderr, exit 0
• Resolved path: full JSON output, exit 0
• Basic commands (echo, direct node -e 'console.log("test")') work fine regardless of path
• The issue specifically affects node processes that load .mjs scripts from under ~/.claude/

Expected

Bash tool should capture stdout from node processes regardless of whether the script path passes through ~/.claude/.

Workaround

Change pwd to pwd -P in the shell wrapper so SCRIPT_DIR resolves to the physical path outside ~/.claude/:

SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd -P)"

Environment

• macOS (Darwin 24.6.0)
• Shell: zsh
• Node: v24.13.0 (via nvm)
• ~/.claude/skills is a symlink to ~/.config/opencode/skills

Related

• #14836 - /skills command doesn't find skills in symlinked directories (same symlink setup, different symptom)