[BUG] Desktop global "Auto-fix CI and address comments" toggle never applies to PRs created via gh from local sessions, and doesn't persist in claude_desktop_config.json

Preflight Checklist

• [x] I have searched existing issues and this is not a duplicate (closest match is #51765, which asked for persistent auto-fix configuration for scheduled remote triggers and was closed as not planned — this report is about the existing global desktop toggle not applying to locally-created PRs and not persisting at all)
• [x] This is a single bug report
• [x] I am using the latest version available to me (desktop app auto-updates; versions below)

What's Wrong?

The Claude desktop app exposes a global settings toggle, "Auto-fix CI and address comments". Enabling it has no observable effect on pull requests created from local desktop sessions via gh pr create:

1. No auto-fix behavior ever triggers on those PRs (CI failures and review comments sit unhandled unless the in-session agent babysits them itself).
2. The toggle's state does not persist anywhere in claude_desktop_config.json — other global toggles do persist there, but after flipping Auto-fix on, no corresponding key appears, and the published docs describe Auto-fix only as a per-PR feature (web-session CI bar, /autofix-pr, or pasting a PR URL).

So the global toggle appears to be a UI affordance with no backing implementation for the local-session + gh-created-PR path.

What Should Happen?

Either:

• Enabling the global toggle should arm auto-fix (CI failure remediation + review-comment handling) for PRs created by local desktop sessions, including ones created with gh pr create; or
• If the toggle is only meant to cover web/cloud sessions, the UI should say so, and the setting should still persist somewhere inspectable.

Error Messages

(none — the behavior simply never triggers; no errors are produced)

Steps to Reproduce

1. In the Claude desktop app settings, enable the global "Auto-fix CI and address comments" toggle.
2. Inspect ~/Library/Application Support/Claude/claude_desktop_config.json: no key reflecting the toggle is written (other global toggles do persist here).
3. In a local desktop session, have Claude create a branch and open a PR via gh pr create on a repo with CI.
4. Push a commit that fails CI (or leave a review comment on the PR).
5. Observe that no auto-fix activity ever occurs on the PR.

Claude Model

Not sure / Multiple models

Is this a regression?

No, this never worked

Claude Code Version

2.1.170 (bundled inside Claude desktop app 1.12603.1)

Platform

Anthropic API

Operating System

macOS (Darwin 25.5.0)

Terminal/Shell

Other (Claude desktop app, local agent session)

Additional Information

• Related but distinct: #51765 requested persistent auto-fix for scheduled remote triggers and was closed as not planned. This report is narrower: the already-shipped global toggle is inert for locally-created PRs and has no persisted state.
• Verified the non-persistence by diffing claude_desktop_config.json before/after flipping the toggle; all other global toggles in the same settings pane persist keys there.
• Current workaround: the in-session agent watches its own PRs (poll gh pr checks / merge-state until terminal) — works, but burns session time on what the toggle implies is automatic.