Stage deleted conflict-resolution files with index.remove, not index.add

[plebioda]

A "deleted by us"/"deleted by them" conflict resolved by removing the file leaves nothing on disk for GitPython's index.add to read, so commit_solution and commit_ci_fix_solution crashed with FileNotFoundError instead of staging the removal.

This is the bug that broke this trigger-merge run: https://github.com/percona/percona-server-mongodb/actions/runs/28846155368/job/85550479497 — the conflict-resolution agent correctly resolved a "deleted by us" conflict on jstests/suites/backup-restore/BUILD.bazel by deleting the file, but commit_solution() then crashed trying to index.add() a path that no longer existed.

Verified fixed with this run, which used the same merge pick but the patched mergai build: https://github.com/plebioda/percona-server-mongodb/actions/runs/28859224967/job/85593343488 — both the merge and publish steps completed successfully.

[Copilot]

Pull request overview

This PR fixes a crash when a conflict/CI-fix “resolved” file is deleted: GitPython’s index.add() can’t stage a path that no longer exists on disk, so the code now stages deletions via index.remove() instead.

Changes:

• Update AppContext.commit_solution() to stage deleted files with index.remove() when item.deleted_file is true.
• Update commit_ci_fix_solution() to split staged paths into “add” vs “remove” based on whether the file exists on disk.
• Add regression tests covering deleted-file staging for both conflict-resolution and CI-fix commits.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
src/mergai/app.py	Stages deletions with index.remove() when a resolved/modified tracked file is deleted.
src/mergai/ci/commit.py	Avoids index.add() on deleted files by staging missing paths via index.remove().
tests/test_commit_solution.py	Adds regression test ensuring commit_solution() properly stages deleted resolved files.
tests/test_ci_fix_commit.py	Adds regression test ensuring commit_ci_fix_solution() properly stages deleted resolved files.

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