fix(warehouse): include tracked deleted files in summary + tracked-paths expansion (PER-186)

libs/beacon/src/beacon/data/skills/contribute-warehouse/scripts/summarize_changes.py

@@ -40,26 +40,55 @@
 # ─────────────────────────────────────────────────────────────────────────────
 
 
+def _git_tracked_or_staged_deleted(warehouse_path: Path, pathspec: str) -> set[str]:
+    """Return tracked paths matching pathspec, INCLUDING staged-for-deletion ones."""
+    found = set()
+    rc, stdout, _ = _run_git(warehouse_path, ["ls-files", "--", pathspec])
+    if rc == 0:
+        for line in stdout.strip().splitlines():
+            if line and ".git" not in Path(line).parts:
+                found.add(line)
+    rc, stdout, _ = _run_git(
+        warehouse_path,
+        ["diff", "--cached", "--name-only", "--diff-filter=D", "--", pathspec],
+    )
+    if rc == 0:
+        for line in stdout.strip().splitlines():
+            if line and ".git" not in Path(line).parts:
+                found.add(line)
+    return found
+
+
 def _expand_pattern(warehouse_path: Path, pattern: str) -> list[str]:
     """Expand a beacon.yaml pattern to concrete relative paths."""
     if "*" in pattern or "?" in pattern:
+        # Glob finds existing files (including untracked)
         matches = glob.glob(str(warehouse_path / pattern), recursive=True)
-        return [
+        paths = {
             str(Path(m).relative_to(warehouse_path))
             for m in matches
             if Path(m).is_file()
             and ".git" not in Path(m).relative_to(warehouse_path).parts
-        ]
+        }
+        # Supplement with tracked files, including staged deletions
+        paths |= _git_tracked_or_staged_deleted(warehouse_path, pattern)
+        return sorted(paths)
 
     p = warehouse_path / pattern
-    if p.is_dir():
-        matches = glob.glob(str(p / "**" / "*"), recursive=True)
-        return [
+    # Treat as directory pattern if it ends with '/' OR the path exists as a dir.
+    # The '/' suffix is the beacon.yaml convention for directories; we must also
+    # handle the case where git rm has removed an empty directory from disk.
+    if pattern.endswith("/") or p.is_dir():
+        matches = glob.glob(str(p / "**" / "*"), recursive=True) if p.exists() else []
+        paths = {
             str(Path(m).relative_to(warehouse_path))
             for m in matches
             if Path(m).is_file()
             and ".git" not in Path(m).relative_to(warehouse_path).parts
-        ]
+        }
+        # Supplement with tracked files, including staged deletions
+        paths |= _git_tracked_or_staged_deleted(warehouse_path, pattern)
+        return sorted(paths)
 
     if p.is_file():
         return [pattern]

libs/beacon/src/beacon/domains/warehouse/_tracked_paths.py

@@ -1,11 +1,22 @@
 """Internal helpers for expanding beacon.yaml tracked paths."""
 
 import glob
+import subprocess
 from pathlib import Path
 
 from beacon.core.manifest.beacon import BeaconManifest
 
 
+def _run_git(warehouse_path: Path, args: list[str]) -> tuple[int, str, str]:
+    """Run a git command inside warehouse, return (returncode, stdout, stderr)."""
+    result = subprocess.run(
+        ["git", "-C", str(warehouse_path)] + args,
+        capture_output=True,
+        text=True,
+    )
+    return result.returncode, result.stdout, result.stderr
+
+
 def get_tracked_paths(warehouse_path: Path, beacon_yaml: Path) -> list[str]:
     """Return the list of beacon.yaml-matched paths relative to warehouse root."""
     if not beacon_yaml.exists():
@@ -30,26 +41,55 @@ def get_tracked_paths(warehouse_path: Path, beacon_yaml: Path) -> list[str]:
     return paths
 
 
+def _git_tracked_or_staged_deleted(warehouse_path: Path, pathspec: str) -> set[str]:
+    """Return tracked paths matching pathspec, INCLUDING staged-for-deletion ones."""
+    found = set()
+    rc, stdout, _ = _run_git(warehouse_path, ["ls-files", "--", pathspec])
+    if rc == 0:
+        for line in stdout.strip().splitlines():
+            if line and ".git" not in Path(line).parts:
+                found.add(line)
+    rc, stdout, _ = _run_git(
+        warehouse_path,
+        ["diff", "--cached", "--name-only", "--diff-filter=D", "--", pathspec],
+    )
+    if rc == 0:
+        for line in stdout.strip().splitlines():
+            if line and ".git" not in Path(line).parts:
+                found.add(line)
+    return found
+
+
 def _expand_pattern(warehouse_path: Path, pattern: str) -> list[str]:
     """Expand a beacon.yaml pattern to concrete relative paths."""
     if "*" in pattern or "?" in pattern:
+        # Glob finds existing files (including untracked)
         matches = glob.glob(str(warehouse_path / pattern), recursive=True)
-        return [
+        paths = {
             str(Path(m).relative_to(warehouse_path))
             for m in matches
             if Path(m).is_file()
             and ".git" not in Path(m).relative_to(warehouse_path).parts
-        ]
+        }
+        # Supplement with tracked files, including staged deletions
+        paths |= _git_tracked_or_staged_deleted(warehouse_path, pattern)
+        return sorted(paths)
 
     p = warehouse_path / pattern
-    if p.is_dir():
-        matches = glob.glob(str(p / "**" / "*"), recursive=True)
-        return [
+    # Treat as directory pattern if it ends with '/' OR the path exists as a dir.
+    # The '/' suffix is the beacon.yaml convention for directories; we must also
+    # handle the case where git rm has removed an empty directory from disk.
+    if pattern.endswith("/") or p.is_dir():
+        matches = glob.glob(str(p / "**" / "*"), recursive=True) if p.exists() else []
+        paths = {
             str(Path(m).relative_to(warehouse_path))
             for m in matches
             if Path(m).is_file()
             and ".git" not in Path(m).relative_to(warehouse_path).parts
-        ]
+        }
+        # Supplement with tracked files, including staged deletions
+        paths |= _git_tracked_or_staged_deleted(warehouse_path, pattern)
+        return sorted(paths)
 
     if p.is_file():
         return [pattern]

libs/beacon/tests/unit/data/skills/contribute_warehouse/test_summarize_changes.py

@@ -524,6 +524,167 @@ def test_no_beacon_package_imports(self):
         )
 
 
+# ─────────────────────────────────────────────────────────────────────────────
+# PER-186: deleted-but-tracked files must appear in summary
+# ─────────────────────────────────────────────────────────────────────────────
+
+
+class TestPer186DeletedTrackedFiles:
+    """PER-186: deleted-but-tracked files must appear in summary."""
+
+    def test_deleted_glob_match_appears_with_deletion_status(self, tmp_path):
+        """Tracked file matching glob pattern, deleted → appears with D status."""
+        warehouse = _make_git_warehouse(tmp_path)
+        beacon_yaml = _write_beacon_yaml(warehouse, ["contexts/*.md"])
+
+        ctx_file = warehouse / "contexts" / "to-delete.md"
+        ctx_file.write_text("# To delete\n")
+        _initial_commit(warehouse, [ctx_file])
+
+        # Delete the file (unstaged deletion)
+        ctx_file.unlink()
+
+        mod = _load_script()
+        result = mod.summarize(warehouse, beacon_yaml)
+        paths = [e["path"] for e in result["tracked_paths"]]
+        assert "contexts/to-delete.md" in paths, (
+            f"PER-186: deleted tracked file should appear. Got: {paths}"
+        )
+
+        entry = next(
+            e for e in result["tracked_paths"] if e["path"] == "contexts/to-delete.md"
+        )
+        assert "D" in entry["git_status"], (
+            f"Expected deletion status, got: {entry['git_status']!r}"
+        )
+
+    def test_deleted_explicit_path_appears_with_deletion_status(self, tmp_path):
+        """Tracked explicit path, deleted → appears with D status."""
+        warehouse = _make_git_warehouse(tmp_path)
+        beacon_yaml = _write_beacon_yaml_full(
+            warehouse, contexts=["contexts/explicit.md"]
+        )
+
+        ctx_file = warehouse / "contexts" / "explicit.md"
+        ctx_file.write_text("# Explicit\n")
+        _initial_commit(warehouse, [ctx_file])
+
+        # Delete the file
+        ctx_file.unlink()
+
+        mod = _load_script()
+        result = mod.summarize(warehouse, beacon_yaml)
+        paths = [e["path"] for e in result["tracked_paths"]]
+        assert "contexts/explicit.md" in paths, (
+            f"PER-186: deleted explicit path should appear. Got: {paths}"
+        )
+
+        entry = next(
+            e for e in result["tracked_paths"] if e["path"] == "contexts/explicit.md"
+        )
+        assert "D" in entry["git_status"], (
+            f"Expected deletion status, got: {entry['git_status']!r}"
+        )
+
+    def test_is_dirty_classifies_unstaged_deletion(self, tmp_path):
+        """PER-186: is_dirty must classify ' D' as dirty."""
+        mod = _load_script()
+        assert mod.is_dirty(" D") is True
+
+    def test_is_dirty_classifies_staged_deletion(self, tmp_path):
+        """PER-186: is_dirty must classify 'D ' as dirty."""
+        mod = _load_script()
+        assert mod.is_dirty("D ") is True
+
+    def test_staged_deletion_glob_match_appears(self, tmp_path):
+        """Tracked file matching glob pattern, git-rm staged → appears with D status."""
+        warehouse = _make_git_warehouse(tmp_path)
+        beacon_yaml = _write_beacon_yaml(warehouse, ["contexts/*.md"])
+
+        ctx_file = warehouse / "contexts" / "to-delete.md"
+        ctx_file.write_text("# To delete\n")
+        _initial_commit(warehouse, [ctx_file])
+
+        # Stage the deletion
+        subprocess.run(
+            ["git", "-C", str(warehouse), "rm", "contexts/to-delete.md"],
+            check=True,
+            capture_output=True,
+        )
+
+        mod = _load_script()
+        result = mod.summarize(warehouse, beacon_yaml)
+        paths = [e["path"] for e in result["tracked_paths"]]
+        assert "contexts/to-delete.md" in paths, (
+            f"PER-186 round 2: staged-deleted tracked file should appear. Got: {paths}"
+        )
+
+        entry = next(
+            e for e in result["tracked_paths"] if e["path"] == "contexts/to-delete.md"
+        )
+        assert "D" in entry["git_status"], (
+            f"Expected deletion status, got: {entry['git_status']!r}"
+        )
+
+    def test_directory_pattern_deletion_appears(self, tmp_path):
+        """Directory pattern (no glob), file deleted unstaged → appears in summary."""
+        warehouse = _make_git_warehouse(tmp_path)
+        beacon_yaml = _write_beacon_yaml_full(warehouse, contexts=["contexts/"])
+
+        ctx_file = warehouse / "contexts" / "nested.md"
+        ctx_file.write_text("# Nested\n")
+        _initial_commit(warehouse, [ctx_file])
+
+        # Delete the file (unstaged)
+        ctx_file.unlink()
+
+        mod = _load_script()
+        result = mod.summarize(warehouse, beacon_yaml)
+        paths = [e["path"] for e in result["tracked_paths"]]
+        assert "contexts/nested.md" in paths, (
+            f"PER-186 round 2: deleted file under directory pattern should appear. Got: {paths}"
+        )
+
+        entry = next(
+            e for e in result["tracked_paths"] if e["path"] == "contexts/nested.md"
+        )
+        assert "D" in entry["git_status"], (
+            f"Expected deletion status, got: {entry['git_status']!r}"
+        )
+
+    def test_directory_pattern_staged_deletion_appears(self, tmp_path):
+        """Directory pattern (no glob), file git-rm staged → appears in summary."""
+        warehouse = _make_git_warehouse(tmp_path)
+        beacon_yaml = _write_beacon_yaml_full(warehouse, contexts=["contexts/"])
+
+        ctx_file = warehouse / "contexts" / "staged-delete.md"
+        ctx_file.write_text("# Staged delete\n")
+        _initial_commit(warehouse, [ctx_file])
+
+        # Stage the deletion
+        subprocess.run(
+            ["git", "-C", str(warehouse), "rm", "contexts/staged-delete.md"],
+            check=True,
+            capture_output=True,
+        )
+
+        mod = _load_script()
+        result = mod.summarize(warehouse, beacon_yaml)
+        paths = [e["path"] for e in result["tracked_paths"]]
+        assert "contexts/staged-delete.md" in paths, (
+            f"PER-186 round 2: staged-deleted file under directory pattern should appear. Got: {paths}"
+        )
+
+        entry = next(
+            e
+            for e in result["tracked_paths"]
+            if e["path"] == "contexts/staged-delete.md"
+        )
+        assert "D" in entry["git_status"], (
+            f"Expected deletion status, got: {entry['git_status']!r}"
+        )
+
+
 # ─────────────────────────────────────────────────────────────────────────────
 # PER-183: get_tracked_paths must walk artifacts.agents (not just skills + contexts)
 # ─────────────────────────────────────────────────────────────────────────────