[BUG] "Yes, allow reading from `<dir>` from this project" no-ops

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other:
• Claude CLI version: 1.0.100 (Claude Code)
• Operating System: macOS 15.6.1
• Terminal: iTerm2

Bug Description

I keep selecting "Yes, allow reading from <dir> from this project", but keep getting prompted about the same <dir>.

Steps to Reproduce

1. Have claude read files from a different directory (e.g. a sibling dir)
2. When prompted, select "Yes, allow reading from <dir> from this project"
3. claude seemingly ignores that response, asks again repeatedly for the same <dir>.

Expected Behavior

claude shouldn't give me this prompt more than once per {session,<dir>} (after I select the option the first time).

Actual Behavior

When I have claude work on other directories, I am getting this prompt repeatedly/constantly (in quick succession, for the same <dir>).

<details><summary>Screenshots: 8 prompts for the same dir, in one session</summary>

<img width="860" height="455" alt="Image" src="https://github.com/user-attachments/assets/40a305ea-d461-4086-8087-d2b9ad190d87" />
<img width="860" height="455" alt="Image" src="https://github.com/user-attachments/assets/abc23eb6-abe9-463b-b510-2d49cc733db4" />
<img width="860" height="455" alt="Image" src="https://github.com/user-attachments/assets/65e00e9c-4e0f-4d8f-b96b-a8cac2e8b74e" />
<img width="860" height="455" alt="Image" src="https://github.com/user-attachments/assets/39c5370d-ed1b-473e-b35b-5766e7b149db" />
<img width="860" height="455" alt="Image" src="https://github.com/user-attachments/assets/6139eddb-bcff-4168-b909-09a82abb3724" />
<img width="860" height="455" alt="Image" src="https://github.com/user-attachments/assets/0e7a6fcd-d850-4829-a59f-206e7e87a0d7" />
<img width="860" height="455" alt="Image" src="https://github.com/user-attachments/assets/c4ca8930-6899-41cf-93ed-b80650cf5b33" />
<img width="860" height="455" alt="Image" src="https://github.com/user-attachments/assets/6b38cc27-f6be-4068-9468-8d39ebaeec49" />
</details>

In this video, I'm prompted about the same dir at :00, :15, and :45:

https://github.com/user-attachments/assets/46014f31-6b37-43d2-bb38-4fc6c898c552

Additional Context

I've been seeing this across many sessions, different initial dirs, different "remote" dirs.

It seems to have started happening around the release (last week?) where I opted in to letting claude train on my sessions.

<details><summary><code>/status</code></summary>

 Claude Code v1.0.98
  L Session ID: 9ab7fa55-5f69-42eb-9275-a4751a86b3e8

 Working Directory
  L /Users/ryan/.rc/py

 Account • /login
  L Login Method: Claude Max Account
  L Organization: ryan@$DOMAIN's Organization
  L Email: ryan@$DOMAIN

 Memory • /memory
  L user: ~/.claude/CLAUDE.md
  L project: ~/.rc/CLAUDE.md

 Model • /model
  L Default Opus 4.1 for up to 50% of usage limits, then use Sonnet 4 (currently Opus)

</details>

      "Read(/Users/ryan/.rc/**)",
      "Read(/Users/ryan/.rc/bash/vars/**)",
      "Read(/Users/ryan/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/.rc/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/thalas/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Bash(python:*)",
      "Bash(.venv/cur/bin/python:*)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Bash(pex:*)",
      "Bash(echo:*)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Read(/Users/ryan/c/oa/marin/**)",
      "Bash(uv python list:*)",
      "Read(/Users/ryan/c/oa/marin/**)",