GitHub MCP server create_or_update_file silently truncates large files

[sayhar]

Bug Description

The GitHub MCP server's create_or_update_file tool silently truncates large files (~500+ lines) when pushing to GitHub. The tool reports success (returns a valid commit SHA and file metadata), but the file content that lands on GitHub is incomplete. No error or warning is produced.

Impact on This Project

Our install.sh script was updated via the MCP create_or_update_file tool. The tool reported success, but the file that landed on GitHub was truncated, breaking the installer for users.

Root Cause

The bug is in github/github-mcp-server (GitHub's official MCP server). An issue has been filed upstream:

Upstream issue: github/github-mcp-server#2182

Reproduction Notes

A controlled test pushing 600 identical comment lines (~72KB) via create_or_update_file did NOT truncate. The truncation appears to be content-dependent — likely triggered by shell script special characters (heredocs, variable expansions, backticks, quotes).

Workaround

For large files (especially shell scripts), use gh api or git push directly instead of the MCP create_or_update_file tool. Always verify file content after pushing via MCP tools.

Severity

High — Silent data loss with a success response.

[SamMorrowDrums]

This appears to be mid-attribution. The GitHub MCP does not apply truncation and Copilot also could find any cause: github/github-mcp-server#2183

So I think you'll need to keep digging to work out what part of the workflow failed you here.

[sayhar]

Note (2026-03-14): The subagent conventions in .claude/subagent.bootup.md now explicitly say to use gh CLI for all GitHub operations, not mcp__github__* tools. This sidesteps the truncation bug. The underlying GitHub MCP bug is upstream and outside our control.\n\nThis issue remains open as a reminder to avoid mcp__github__create_or_update_file for large files.

[sayhar]

Triage note (2026-03-15): This is a bug in GitHub's official MCP server (github/github-mcp-server), not in Lobster itself. The workaround — using gh CLI for all GitHub write operations — is now the established practice and is documented in subagent.bootup.md ('Use gh CLI for all GitHub operations — posting PR reviews, merging PRs, creating issues, etc. Do NOT use mcp__github__* MCP tools in agent code'). This guidance effectively prevents hitting the bug in normal operation.

Recommend closing as 'won't-fix' from Lobster's perspective — the upstream bug exists but Lobster has mitigated it through tooling guidance. Alternatively, keep open as a tracking issue until the upstream bug is fixed in github-mcp-server.

[sayhar]

Closing as won't-fix from Lobster's perspective. The bug is in GitHub's official github-mcp-server (upstream). Lobster's mitigation — 'Use gh CLI for all GitHub write operations; do NOT use mcp__github__* MCP tools in agent code' — is now documented in subagent.bootup.md and is the established practice. Agents no longer use create_or_update_file for file operations. If this upstream bug is fixed, no changes are needed in Lobster.