[BUG] constant permission requests and preference of Bash() calls over built-in tools

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?

For git calls (not github), Claude wants to use Bash() to run them. Even though I have a git MCP server. I have to keep telling it "use built-in tools". Happens often from agent (Explore) run.

This is also the case with preference for Bash(awk/sed/find/grep) over built-in Search/Read tools. Again, "prefer built-in tools" will fix it for an agent run, but I have to do this for every run.

Doesn't matter that I have a directive about this in my Claude.md user memory.

What Should Happen?

Claude should have built-in tools for git so that "allow things like this" can match git commands.

Error Messages/Logs

Steps to Reproduce

ask a question that causes an explore agent to spin up and go looking in the repo. You'll get prompted for many things, which cannot be matched by a "Yes, and allow all like this"

Same thing if you ask for some git operation (commit and push). You'll get prompted for each git command and some wont be able to be allowed in the future because of the matching wildcard issue.

Claude Model

None

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.84

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_