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

Reproduce los fallos mediante el GitHub MCP connector usando las operaciones indicadas de archivo, rama y varios archivos; después, compara el commit SHA informado con la rama remota y git log. Captura el estado de API/tree y los errores de análisis de JSON; la tarea estará terminada cuando los commits lleguen de forma fiable a la rama remota de destino con los archivos y el mensaje especificados, sin resultados parciales ni resultados únicamente locales.

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.