[BUG] "Pull request status couldn't be checked" warning appears permanently even with no open PRs

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?

The red warning banner "Pull request status couldn't
be checked and may be out of date" appears at the
start of every session even though:

• There are no open pull requests
• There are no stale branches (only origin/main exists)
• CLAUDE.md instructs direct commits to main only
• The project has never had an open PR

The warning cannot be dismissed permanently and
reappears every session. Clicking ✕ only dismisses
it for that session.

What Should Happen?

The "Pull request status couldn't be checked and may
be out of date" warning banner should not appear when
there are no open pull requests and no stale branches
in the repository. Or it should stay dismissed after
clicking the ✕ button rather than reappearing every
session.

Error Messages/Logs

Warning message displayed: "Pull request status 
couldn't be checked and may be out of date."

Context:
- Repository: github.com/pdemoor/cloudbop
- No open pull requests (confirmed at github.com/pdemoor/cloudbop/pulls)
- Only one remote branch exists: origin/main
- CLAUDE.md instructs direct commits to main only
- Warning reappears every session regardless of 
  clicking the ✕ dismiss button
- Warning is purely cosmetic but cannot be 
  permanently suppressed

Steps to Reproduce

1. Create a new Claude Code project connected to a

GitHub repository

1. Claude Code creates a pull request during a session
2. The PR is subsequently closed or merged on GitHub
3. In every future Claude Code session, the red warning

banner appears: "Pull request status couldn't be
checked and may be out of date"

1. Clicking the ✕ dismiss button removes it for that

session only

1. On next session launch the warning reappears
2. Confirmed no open PRs exist at github.com/pdemoor/cloudbop/pulls
3. Confirmed only origin/main branch exists (git branch -r)
4. Warning cannot be permanently dismissed

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

claude --version

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

The warning "Pull request status couldn't be checked
and may be out of date" appears on every session start
in the Claude Code UI (not the terminal).

Confirmed clean state:

• No open PRs: github.com/pdemoor/cloudbop/pulls is empty
• Only origin/main branch exists
• CLAUDE.md added with instruction to never create PRs
• Warning persists across sessions regardless

The warning banner has an ✕ button but clicking it
only dismisses for the current session. It reappears
on every new session launch.

Repository: https://github.com/pdemoor/cloudbop