[BUG] "Allow for all projects" permission not applied to pending MCP requests in same session

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?

When multiple MCP tool permission requests are queued in the same session, selecting "Allow for all projects" (global/user scope) only approves the current request. Pending permission requests are not automatically approved despite matching the global permission rule that was just created.

Platform-Specific: This issue occurs in the VSCode Extension on Windows. The CLI behavior has not been tested.

Steps to Reproduce

1. Install Claude Code VSCode Extension (v2.1.76) on Windows
2. Configure any MCP server (tested with multiple MCP servers)
3. Start a Claude Code session in VSCode integrated terminal
4. Request a task that triggers multiple MCP tool calls simultaneously

Example: "List all issues in Linear and check PRs in GitHub"

1. First permission prompt appears → Click "Allow for all projects"
2. Second permission prompt immediately appears (should be auto-approved but isn't)
3. Third permission prompt appears (should be auto-approved but isn't)
4. Each pending request requires manual approval despite global permission being granted

Note: This affects ALL MCP servers, not server-specific.

Expected Behavior

When "Allow for all projects" is selected, the permission rule should be:

• Immediately stored in ~/.claude/settings.json (this happens ✓)
• Immediately applied to ALL pending permission requests in the queue
• All subsequent MCP tools in the same session should be auto-approved

The permission system should either:

1. Apply the newly granted global permission to all pending requests in the queue, OR
2. Batch multiple permission requests and prompt once for all of them

Error Messages/Logs

No error messages - the tools execute after manual approval. The issue is the redundant permission prompts.

Claude Model

Any model (reproduces regardless of model used)

Is this a regression?

I don't know - unable to test earlier versions

Last Working Version

Unknown

Claude Code Version

2.1.76

Platform

VSCode Extension

Operating System

Windows (VSCode Extension) / Linux (CLI - not relevant to this bug)

Terminal/Shell

VSCode integrated terminal

Additional Information

Related Issues:

• #34739 - MCP Permission Wildcards Not Working
• #28127 - Wildcard Permission Matching Fails
• #17017 - Project-level Permissions Replace Global Instead of Merging

Distinction from Related Issues:
This is NOT a session-to-session persistence issue (those are covered in #26765, #24433, #21080). This is specifically about the SAME session where a global permission is granted but not applied to pending requests.

Severity: Medium - Causes repetitive permission prompts when working with MCP servers that have multiple tools or when tasks trigger parallel MCP calls.

Willingness to Contribute:
If the team is open to external contributions for this fix, I am ready and willing to help implement a solution. Please let me know if there's a process for contribution or if this is handled internally.