Add patch-safe exact file update tool

[jasonobrown]

Summary

Adds apply_file_patch, a bounded exact-text update tool that lets the GitHub MCP server modify an existing UTF-8 file without requiring the MCP client/model to resend the entire replacement file.

Closes #3231.

Motivation

The existing create_or_update_file / push_files interfaces require complete replacement content. A real ~303 KB changelog update was truncated upstream of GitHub while only a small insertion was intended. The resulting branch commit was detected and discarded, but recovery required a separate local Git client.

This tool keeps the large file server-side and sends only the intended exact replacements through MCP.

Safety model

• Requires an exact current branch expected_head_sha.
• Requires the exact existing expected_blob_sha for the target file.
• Each old_text must match exactly expected_occurrences times at that step; default is one.
• No fuzzy patching or offset guessing.
• Rejects empty match strings, no-op updates, symlinks, non-regular modes, non-UTF-8 data, oversized files, oversized patch payloads, and excessive edit counts.
• Preserves regular/executable file mode.
• Creates the replacement blob/tree/commit on the exact expected parent.
• Advances the branch ref with force=false; concurrent branch movement fails non-fast-forward instead of overwriting it.
• Existing workflow-file OAuth challenge behavior is preserved.

Initial limits are 4 MiB target file, 256 KiB aggregate old/new patch text, and 100 ordered edits.

Tests

Includes focused unit coverage for ordered exact replacement, occurrence-count mismatch, empty match rejection, no-op rejection, and patch-size bounding.

I could statically verify the go-github/v89 Git API call signatures available from repository/dependency source, but this execution environment cannot clone the complete public repository to run the full Go suite locally. This PR is therefore intentionally draft until repository CI/build/snapshot/documentation checks establish the exact integration result. I will address concrete CI findings without weakening the fail-closed contract.