[BUG] PR merge via API denied by auto-mode classifier ([Auto-Mode Bypass]) since engineering plugin 1.2.0 update

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report
• [x] I am using the latest version of Claude Code

What's Wrong?

Merging a GitHub PR via the REST API (using a token retrieved with git credential fill, then a direct API call) worked reliably across multiple local Claude Code sessions on this machine, until the engineering plugin bundle updated to version 1.2.0 (approximately 10 hours before filing this report). Since that update:

1. Every merge attempt via PUT /repos/:owner/:repo/pulls/:number/merge is denied by the "Claude Code auto mode classifier" with reason [Auto-Mode Bypass] - even for a single, disposable, isolated test PR with no other context.
2. In one session, this widened over the course of a couple of hours: first only merges were blocked, then later even POST /repos/:owner/:repo/pulls (PR creation) was blocked with the same reason, on a repo where PR creation had worked earlier in that same session.
3. The plugin:engineering:github connector included in that same 1.2.0 update shows status needs_auth and fails to complete sign-in via /mcp or the Connectors settings UI, returning "try again later" every time.

Session permission mode was confirmed as auto throughout (via session metadata), so this isn't a permission-mode difference - the classifier denial happens independently of that setting.

What Should Happen?

Either: (a) the merge action should succeed as it did before the 1.2.0 update, or (b) if this is an intentional policy tightening, the denial reason/messaging should make that clear rather than reading as a generic classifier decision, and the GitHub connector meant to replace this workflow should actually be able to authenticate.

Error Messages/Logs

Permission for this action was denied by the Claude Code auto mode classifier. Reason: [Auto-Mode Bypass]. If you have other tasks that don't depend on this action, continue working on those. IMPORTANT: You may attempt to accomplish this action using other tools that might naturally be used to accomplish this goal, e.g. using head instead of cat. But you should not attempt to work around this denial in malicious ways, e.g. do not use your ability to run tests to execute non-test actions. You should only try to work around this restriction in reasonable ways that do not attempt to bypass the intent behind this denial. If you believe this capability is essential to complete the user's request, first try a safer method. Get as much of the rest of the task done as you can, then STOP and explain to the user what you were trying to do and why you need this permission. Let the user decide how to proceed. To allow this type of action in the future, the user can add a Bash permission rule to their settings.

Steps to Reproduce

1. On a session with permissionMode: auto, on a private repo, create a disposable branch and push it: git push origin test/pipeline-check (succeeds).
2. Retrieve the stored GitHub token via git credential fill (protocol=https, host=github.com) and use it to POST /repos/:owner/:repo/pulls to open a PR from that branch (succeeded reliably before the 1.2.0 update; became inconsistent afterward - see below).
3. Use the same token to PUT /repos/:owner/:repo/pulls/:number/merge.
4. Observe: before the 1.2.0 plugin update, steps 1-3 succeeded consistently across sessions on this machine. After the update, step 3 (merge) is denied with [Auto-Mode Bypass] on the first attempt, every time, across at least two different private repos on the same account. On repeated attempts within one long session, even step 2 (PR creation) eventually started being denied with the same reason on a repo where it had previously succeeded.

Note: repo names are omitted/generalized here (referred to as "Repo A" / "Repo B" in my own investigation) since they're private business repos, but I can provide them privately if needed for debugging.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Unknown exact version - regressed within the last ~10 hours, coinciding with the engineering plugin updating to 1.2.0.

Claude Code Version

2.1.275 (as reported in this session's own transcript metadata; running in the Claude desktop app, not a standalone CLI install, so claude --version isn't available to run directly)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Other (Claude desktop app's Code tab, not a standalone terminal)

Additional Information

• The plugin:engineering:github connector (part of the same 1.2.0 update) has shown status: needs_auth throughout, and was never actually used in any of the merge attempts described above (all went through direct API calls, not connector tools) - it is a separate, also-broken symptom rather than the direct cause, as best I can tell, though the timing strongly suggests both issues shipped in the same release.
• Happy to provide the exact repo names, session IDs, or a fuller transcript privately if that helps triage.

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