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

Reproduziere die Fehler über den GitHub MCP connector mithilfe der aufgeführten Datei-, Branch- und Mehrdatei-Operationen und vergleiche anschließend die gemeldete Commit-SHA mit dem Remote-Branch und git log. Erfasse den API-/Tree-Zustand und die JSON-Parsing-Fehler; abgeschlossen ist die Aufgabe, wenn Commits zuverlässig den Ziel-Remote-Branch mit den angegebenen Dateien und der angegebenen Nachricht erreichen, ohne Teilergebnisse oder ausschließlich lokale Ergebnisse.

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.