git_commit during a merge records one parent and leaves MERGE_HEAD in place
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调研方向
该 bug 位于 src/git/src/mcp_server_git/server.py，原因是 git_commit 调用 repo.index.commit() 时未处理合并状态。首先检查该函数以及 GitPython 的 IndexFile.commit() 方法签名。当 MERGE_HEAD 存在时，读取其对应的提交并作为 parent_commits 传入，随后清除 MERGE_HEAD、MERGE_MSG 和 MERGE_MODE。在 git 测试套件中添加一个测试：执行带 --no-commit 参数的合并操作，调用 git_commit，并断言存在两个父提交且无剩余合并状态。
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描述
Describe the bug
git_commit cannot conclude a merge. While a merge is in progress (MERGE_HEAD present, e.g. after git merge --no-commit or a resolved conflict), it writes a commit with one parent, HEAD, and leaves MERGE_HEAD (and MERGE_MSG) in place, so the repository stays in merge state and the merged branch's history is not recorded.
src/git/src/mcp_server_git/server.py, git_commit calls repo.index.commit(message). GitPython's IndexFile.commit() takes parent_commits=None, which means [repo.head.commit] only; it neither reads nor clears MERGE_HEAD.
Found in the Copilot review of #5007 (the fix for #4762), which keeps the empty-merge-commit case committable but, like the code before it, records it with one parent. This predates #5007: any merge resolved through git_commit has always been recorded this way.
To Reproduce
import git
# repo on main with a branch `side` that adds side.txt
repo.git.merge("side", "--no-commit", "--no-ff")
commit = repo.index.commit("merge side") # what git_commit does
len(commit.parents) # 1, git commit would give 2
(Path(repo.git_dir) / "MERGE_HEAD").exists() # True, merge still in progress
Expected behavior
While MERGE_HEAD is present, git_commit records HEAD plus every MERGE_HEAD commit as parents and clears the merge state, as git commit does (either by shelling out to git commit, or by passing parent_commits and removing MERGE_HEAD/MERGE_MSG/MERGE_MODE). A test asserts both parents and that MERGE_HEAD is gone.
Additional context
Related: #659 (a git_merge tool), which would make this path reachable from the server alone.
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