Worktree-isolation Bash guard overrides an explicit PreToolUse `permissionDecision: allow`

Summary

In a worktree-isolated agent, the Bash command guard refuses a command that a PreToolUse hook explicitly allowed
("permissionDecision":"allow"). The hook's verdict is recorded in the transcript, and the refusal follows it. No
setting, permission rule, or hook output lets a user override the guard for a command they have judged safe.

Version: 2.1.292, macOS (darwin arm64).

Repro

1. Install a PreToolUse hook on Bash that returns

{"hookSpecificOutput":{"hookEventName":"PreToolUse","permissionDecision":"allow"}} for the command below.

1. Spawn an agent with isolation: worktree that writes .claude/tmp/guardtest/x.awk (BEGIN{print "awk ran"}) and

in.txt with the Write tool, then runs:
awk -f .claude/tmp/guardtest/x.awk .claude/tmp/guardtest/in.txt

Observed

The transcript's hook_success attachment for the call shows the hook's permissionDecision":"allow". The tool result
is:

This agent is isolated in the worktree …/agent-a8422017222635263, but this command runs awk with -f in a plain command, so what it runs cannot be shown not to be git. Refusing to run it — a worktree-isolated agent's git operations must target its own worktree. Run the plain command from …/agent-a8422017222635263.

The same refusal followed an explicit hook allow for /usr/bin/awk -f …, absolute-path awk -f …, and
cat x.awk | awk -f - ….

Control: the identical command, with the same hook allow, in the main session (no worktree) prints awk ran.

Expected

An explicit PreToolUse allow is the user's decision about that command, and the harness honours it — or, at minimum,
there is a documented setting that lets it take precedence over the worktree command guard.

Related

Other reports of the guard refusing git-free commands: #94040, #95122, #97225, #97474, #93193. This report is
narrower: the command was not merely git-free, the user's own hook explicitly allowed it. #93193 states the block fires
before any PreToolUse hook runs; the transcripts here show the hook ran and returned allow, and the refusal came after.