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

src/mergai/app.py

@@ -658,10 +658,16 @@ def commit_solution(self):
         for item in self.repo.index.diff(None):
             path = item.a_path
             if path in resolved:
-                self.repo.index.add([path])
+                if item.deleted_file:
+                    self.repo.index.remove([path])
+                else:
+                    self.repo.index.add([path])
             elif path in declared_modified:
                 modified_files.append(path)
-                self.repo.index.add([path])
+                if item.deleted_file:
+                    self.repo.index.remove([path])
+                else:
+                    self.repo.index.add([path])
             else:
                 message = (
                     f"Unstaged changes found in file {path}, which the "

src/mergai/ci/commit.py

@@ -6,6 +6,7 @@
 keeps a thin delegator.
 """
 
+import os
 from typing import Any
 
 from ..solution_types import CI_FIX
@@ -67,10 +68,23 @@ def commit_ci_fix_solution(app: Any, solution_idx: int) -> None:
     # Stage every file the agent touched (resolved + modified).
     # Untracked files won't show up in index.diff(None), so add them
     # explicitly via git index.add — same approach commit_solution uses.
+    # A file the agent deleted to resolve a conflict no longer exists on
+    # disk, so it must be staged via index.remove instead — index.add
+    # would try to read it and raise FileNotFoundError.
     files_to_stage = list(response.get("resolved", {}).keys())
     files_to_stage += list(response.get("modified", {}).keys())
-    if files_to_stage:
-        app.repo.index.add(files_to_stage)
+    working_dir = app.repo.working_tree_dir or ""
+    files_to_add = []
+    files_to_remove = []
+    for f in files_to_stage:
+        if os.path.exists(os.path.join(working_dir, f)):
+            files_to_add.append(f)
+        else:
+            files_to_remove.append(f)
+    if files_to_add:
+        app.repo.index.add(files_to_add)
+    if files_to_remove:
+        app.repo.index.remove(files_to_remove)
 
     # Build commit message matching mergai's voice. The title is
     # configurable (commit.ci_fix_title_format) so it can mirror the PR

tests/test_ci_fix_commit.py

@@ -0,0 +1,69 @@
+"""Tests for commit_ci_fix_solution staging behavior.
+
+Regression coverage mirroring tests/test_commit_solution.py: when the agent
+resolves a CI failure by deleting a file, staging must use index.remove
+instead of index.add, since the file no longer exists on disk for add to
+read.
+"""
+
+from types import SimpleNamespace
+
+import git
+
+from mergai.ci.commit import commit_ci_fix_solution
+from mergai.solution_types import CI_FIX
+
+
+def _init_repo(path):
+    repo = git.Repo.init(path)
+    with repo.config_writer() as cw:
+        cw.set_value("user", "name", "test")
+        cw.set_value("user", "email", "test@example.com")
+    (path / "a.txt").write_text("base a\n")
+    repo.index.add(["a.txt"])
+    repo.index.commit("init")
+    return repo
+
+
+def _fake_app(repo, *, resolved):
+    head = repo.head.commit.hexsha
+    note = SimpleNamespace(
+        has_solutions=True,
+        solutions=[
+            {
+                "type": CI_FIX,
+                "request": {"workflow": "format", "run_id": "1", "attempt_number": 1},
+                "response": {"summary": "fix", "resolved": resolved, "modified": {}},
+            }
+        ],
+        merge_info=SimpleNamespace(target_branch="master", merge_commit_sha=head),
+    )
+    config = SimpleNamespace(
+        workflows={},
+        commit=SimpleNamespace(
+            ci_fix_title_format="Fix '%(workflow)' failure for merge commit "
+            "'%(merge_commit_short_sha)' into '%(target_branch)'"
+        ),
+    )
+    return SimpleNamespace(
+        note=note,
+        repo=repo,
+        config=config,
+        commit_footer="",
+        add_selective_note=lambda *a, **k: None,
+    )
+
+
+def test_commit_ci_fix_solution_stages_deleted_resolved_file(tmp_path):
+    repo = _init_repo(tmp_path)
+
+    # The agent resolved the CI failure by deleting the offending file.
+    (tmp_path / "a.txt").unlink()
+
+    app = _fake_app(repo, resolved={"a.txt": "removed stale file"})
+
+    commit_ci_fix_solution(app, 0)
+
+    assert not repo.is_dirty()
+    assert "a.txt" not in [item[0] for item in repo.index.entries]
+    assert not (tmp_path / "a.txt").exists()

tests/test_commit_solution.py

@@ -68,6 +68,26 @@ def test_commit_solution_accepts_declared_modified_files(tmp_path, monkeypatch):
     assert (tmp_path / "version.h").read_text() == "adjusted v\n"
 
 
+def test_commit_solution_stages_deleted_resolved_file(tmp_path, monkeypatch):
+    repo = _init_repo(tmp_path)
+    monkeypatch.chdir(tmp_path)
+
+    # Conflict resolved by deleting the file (e.g. a "deleted by us" conflict
+    # where the deletion side wins) — commit_solution must stage the removal
+    # via index.remove instead of trying to index.add a path that no longer
+    # exists on disk.
+    (tmp_path / "a.txt").unlink()
+
+    app = AppContext()
+    app._note = _note(repo, resolved={"a.txt": {}}, modified={})
+
+    app.commit_solution()
+
+    assert not repo.is_dirty()
+    assert "a.txt" not in [item[0] for item in repo.index.entries]
+    assert not (tmp_path / "a.txt").exists()
+
+
 def test_commit_solution_rejects_undeclared_dirty_file(tmp_path, monkeypatch):
     repo = _init_repo(tmp_path)
     monkeypatch.chdir(tmp_path)