[BUG] Edit permission prompt still fires despite bare Edit/Edit(**) allow rules and global bypassPermissions mode

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?

Claude Code repeatedly shows the "Make this edit to [file]?" confirmation prompt on Edit tool calls even though:

The project's .claude/settings.json has both bare Edit and Edit(**) in the permissions.allow list
The global ~/.claude/settings.json has "defaultMode": "bypassPermissions" set
No ask or deny rule matches Edit anywhere in the effective config (project, project-local, or global)
Per Claude Code's own permission precedence (deny → ask → allow, first match wins), this combination should never prompt. It happened 5 times in one day across unrelated files (inc/hooks/grid-lines-toggle.php, scripts/sftp-push.js, inc/helpers/work-portfolio-grid-render.php, etc.), including once mid-session with several unrelated apps/windows open — ruling out a focus or window-state trigger. Config was manually re-verified correct after each occurrence; no rule gap was ever found. Suspected cause: in-memory permission-cache staleness not syncing with the on-disk settings files.

What Should Happen?

once a matching allow rule exists for Edit (bare or Edit(**)) in an effective settings file — or defaultMode is set to bypassPermissions — an Edit tool call should apply silently, with no confirmation prompt, for every subsequent edit in that session and in future sessions, until the config changes or a deny/ask rule intervenes.

Error Messages/Logs

Steps to Reproduce

In a project's .claude/settings.json, set permissions.allow to include "Edit" and "Edit()".
In ~/.claude/settings.json (global), set "permissions": { "defaultMode": "bypassPermissions", ... }.
Start a Claude Code session in that project (VS Code extension, this case) and work normally over an extended session — multiple file edits across different files/directories within the project, interspersed with other tool calls (Bash, Read, etc.), possibly with other applications/windows also open and in focus at various points.
At some point, unpredictably, an Edit call to a file in the project triggers the "Make this edit to [file]?" confirmation prompt instead of applying silently.
Re-check the effective config immediately after the prompt appears (/permissions, or read the settings files directly) — the same Edit/Edit() allow rule and bypassPermissions mode are still present and correctly formatted; no deny/ask rule matches.
Frequency observed: 5 times in a single day, on unrelated files, with no consistent trigger identified (not tied to file path, file type, time since last edit, or app focus state).

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.220 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_