Prevent raw Git LFS files from being committed through the API - #2015

Summary

The commit_files tool writes files through the GitHub Git Data API. When a checkout marks a file with filter=lfs, this path can put the raw file in the tree where Git expects an LFS pointer.

Check Git's working-tree and index attributes before making API requests. If any requested file is LFS-tracked, reject the whole batch with the file name and direct the caller to the Git CLI flow. Ordinary files and workflows without a local checkout keep their existing behavior. The commit-signing docs explain how to configure Git LFS with the Git CLI and how to use SSH signing if signatures are required.

Fixes #91.

Verification

• The regression test failed on main and passed with the change. It calls the actual MCP server against a loopback GitHub API fixture. It verifies that a mixed batch makes zero API requests, an unstaged edit removing the LFS rule does not bypass the index check, and ordinary commits still succeed.
• On a GitHub-hosted runner, the Git CLI produced an LFS pointer, uploaded the object to a local bare remote, and recovered the original bytes in a fresh clone.
• All 1,226 hosted tests, TypeScript, and Prettier passed. Hosted verification