Read(./.entire/metadata/**) deny rule makes ordinary commands ask for approval, breaking auto/unattended permission modes

What happened?

entire enable installs Read(./.entire/metadata/**) into permissions.deny in .claude/settings.json (and .factory/settings.json). It was meant as "ignore this data" rule so an agent searching for something would not find prior session logs and consults them, but a deny rule is a hard block and claude code blocks now on these in automode.

Symptom: any recursive read from the repo root — grep -r, and even commands that only name the path like git check-ignore .entire/metadata — is refused and needs manual approval. Deny rules can't be auto-approved, so auto mode and unattended runs stop on them.

Example:

Read(./.entire/metadata/**) deny rule makes ordinary commands ask for approval, breaking auto/unattended permission modes

 Do you want to proceed?
   ❯ 1. Yes
     2. No

Cause: Claude Code applies Read deny rules to file-reading Bash commands too, and rules resolve deny → ask → allow with no allowlist exceptions (docs).

The rule wasn't buying much: it guarded a staging buffer, not the durable copy (transcripts live in the checkpoint tree, readable via git show entire/checkpoints/v1:...), and .entire/.gitignore already lists metadata/, which Claude Code's Grep honors.

Fix in flight: #2258 stops installing it, and entire doctor removes it from existing repos. A session-start notice points there.

Workaround now: delete that line from .claude/settings.json, or run entire doctor once #2258 lands.

Steps to reproduce

No response

Entire CLI version

v0.10.4 and before

OS and architecture

No response

Agent

Claude Code

Terminal

No response

Logs / debug output

Additional context

No response