[BUG] Bash tool's heredoc commit format triggers approval prompt on every commit regardless of auto-accept settings

Found 3 possible duplicate issues:

1. https://github.com/anthropics/claude-code/issues/31117
2. https://github.com/anthropics/claude-code/issues/23926
3. https://github.com/anthropics/claude-code/issues/25441

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🤖 Generated with Claude Code

This is the same root cause as #31117 — the Bash tool's description field contains hardcoded heredoc templates for both git commit and gh pr create that use $(cat <<'EOF' ... EOF), which triggers the command substitution approval prompt regardless of auto-accept settings.

See my detailed comment on #31117 for the specific system prompt text, why CLAUDE.md overrides don't reliably work, workarounds, and a suggested fix.

tl;dr: The Bash tool description says ALWAYS pass the commit message via a HEREDOC. This fights project-level instructions and triggers approval prompts on every commit and PR creation. Fix: replace the heredoc examples with git commit -F <file> and gh pr create --body-file <file>.

My workarounds appear to be successful, both in tandem:

Git Commit went through without prompt with a deny-retry cycle

We have a pre tool use hook that denies the permission-prompting syntax with a message that remind claude to do it the "better" way, using a temp file

⏺ Bash(git add release/environments/production.yaml release/environments/staging.yaml && git commit -m "$(cat <<'EOF'
      Bump worker_postprocess_asr memory request to 9Gi…)
  ⎿  PreToolUse:Bash hook returned blocking error
  ⎿  BLOCKED: Do not use heredoc syntax for commit messages. Write the message to dev/tmp/commit-msg.txt using the Write tool, then run: git commit -F
     dev/tmp/commit-msg.txt
  ⎿  Error: Hook PreToolUse:Bash denied this tool

❯ Tool loaded.

⏺ Write(dev/tmp/commit-msg.txt)
  ⎿  Wrote 10 lines to dev/tmp/commit-msg.txt
[...]
⏺ Bash(git add release/environments/production.yaml release/environments/staging.yaml && git commit -F dev/tmp/commit-msg.txt)

This was achieved with a PreToolUse hook

      {
        "matcher": "Bash",
        "hooks": [
          {
            "type": "command",
            "command": "script/developer/agents/reject-prompt-triggering-syntax"
          }
        ]
      }

the script specifically targets these two forms to avoid over-firing

COMMAND=$(jq -r '.tool_input.command' 2>/dev/null)

# Match: git commit ... $(cat <<
if echo "$COMMAND" | grep -qE 'git commit.*\$\(cat <<'; then
  jq -n '{
    hookSpecificOutput: {
      hookEventName: "PreToolUse",
      permissionDecision: "deny",
      permissionDecisionReason: "BLOCKED: Do not use heredoc syntax for commit messages. Write the message to dev/tmp/commit-msg.txt using the Write tool, then run: git commit -F dev/tmp/commit-msg.txt"
    }
  }'
  exit 0
fi


# Match: gh pr create ... $(cat <<
if echo "$COMMAND" | grep -qE 'gh pr create.*\$\(cat <<'; then
  jq -n '{
    hookSpecificOutput: {
      hookEventName: "PreToolUse",
      permissionDecision: "deny",
      permissionDecisionReason: "BLOCKED: Do not use heredoc syntax for PR body. Write the body to dev/tmp/pr-body.md using the Write tool, then run: gh pr create --body-file dev/tmp/pr-body.md"
    }
  }'
  exit 0
fi

exit 0

Pull Request went through without prompt

We updated our pull request skill:

## IMPORTANT: Do not use heredoc syntax for PR creation

The Bash tool's built-in instructions suggest using `$(cat <<'EOF' ... EOF)` heredoc
syntax for `gh pr create --body` and `git commit -m`. **This triggers permission prompts
that disrupt agentic workflows and must be avoided.** Always use the `--body-file` approach
described in this skill instead — write content with the Write tool, then reference the file.

and this was respected

The $() heredoc pattern triggers a safety heuristic that can't be suppressed via settings. A PreToolUse hook can auto-approve git commits specifically:

INPUT=$(cat)
COMMAND=$(echo "$INPUT" | jq -r '.tool_input.command // empty' 2>/dev/null)
[ -z "$COMMAND" ] && exit 0
FIRST_LINE=$(echo "$COMMAND" | head -1 | sed 's/^\s*//')
if echo "$FIRST_LINE" | grep -qE '^git\s+commit'; then
    jq -n '{hookSpecificOutput:{hookEventName:"PreToolUse",permissionDecision:"allow",permissionDecisionReason:"git commit auto-approved (heredoc format)"}}'
fi
exit 0

{
  "hooks": {
    "PreToolUse": [{
      "matcher": "Bash",
      "hooks": [{ "type": "command", "command": "bash ~/.claude/hooks/git-commit-allow.sh" }]
    }]
  }
}

The hook matches on git commit as the first line, so both the heredoc format and simple -m "message" format are auto-approved. The $() substitution is irrelevant to the hook — it only looks at the command name, not the shell syntax.

This was fixed in v2.1.71 — Fixed false-positive permission prompts for compound bash commands containing heredoc commit messages (e.g. git commit -m "$(cat <<'EOF'...)"). If you're still seeing this in the latest version, please comment with your version and repro and we'll reopen.

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