Intermittent commit/push failures when using GitHub MCP connector for file operations and branch management, via Grok official Connector

### Describe the bug

When using the GitHub MCP connector (via Grok / xAI interface) to perform write operations on a repository, commits and pushes frequently fail or apply only locally. Changes appear successful in the tool response but did not reach the remote branch.

### Affected Version / Environment
- MCP Host: Grok (xAI) with GitHub MCP connector
- Repository: jacob-kraniak/the-book-of-secret-knowledge (fork of trimstray/the-book-of-secret-knowledge)
- Branch: JK_Revisions
- Operation types failing:
- Creating/updating files (`.pre-commit-config.yaml`, Python scripts, Markdown files)
- Deleting branches
- Multi-file refactors

### Steps to Reproduce
1. Instruct the MCP agent to create or modify files (e.g., "Add .pre-commit-config.yaml with specific hooks").
2. Instruct the agent to commit the changes with a descriptive message.
3. Refresh the GitHub repository page or check `git log` on the remote.
4. Observe that the commit either does not appear or shows as "incomplete" / missing files.

### Expected Behavior
Commits should reliably push to the target remote branch with the specified files and message.

### Actual Behavior
- Tool reports success and provides a commit SHA.
- Remote repository shows no new commits or partial state.
- Errors observed: "API/tree state errors", "JSON parsing issues", silent failures.
- Some operations succeed (e.g., earlier extractions), while others fail consistently.

### Additional Context / Observations
- Failures are intermittent but frequent during heavy Markdown refactoring sessions.
- Local-only changes sometimes occur (visible only in the agent's working context).
- This has occurred multiple times over the past few hours (May 15, 2026) while reorganizing a knowledge repository. Further experienced across other repos over the past few weeks.
- Similar issues reported by other users with MCP GitHub connectors.