fix(workflows): match overlay file extensions case-insensitively

src/specify_cli/workflows/overlay/layer_sources.py

@@ -147,7 +147,12 @@ def collect(self, workflow_id: str, *, include_disabled: bool = False) -> list[L
                 workflow_overlay_dir, [f"Cannot enumerate overlays: {exc}"]
             ) from exc
         for path in entries:
-            if not path.is_file() or path.suffix not in (".yml", ".yaml"):
+            # Match the extension case-insensitively. A hand-placed overlay
+            # named ``<id>.YML`` or ``<id>.Yaml`` was skipped here and never
+            # applied, with nothing reported to say the file had been ignored.
+            # Every other YAML discovery path in the package already lowercases
+            # before matching (``WorkflowEngine``, ``workflow add`` / ``run``).
+            if not path.is_file() or path.suffix.lower() not in (".yml", ".yaml"):
                 continue
             if path.is_symlink():
                 raise OverlayLoadError(path, ["Symlinked overlay files are not allowed"])

src/specify_cli/workflows/overlay/operations.py

@@ -106,7 +106,11 @@ def _find_overlay_file(project_root: Path, workflow_id: str, overlay_id: str) ->
         return None
     matches: list[Path] = []
     for path in entries:
-        if not path.is_file() or path.suffix not in (".yml", ".yaml"):
+        # Must match ``ProjectOverlaySource.collect`` exactly. With the loader
+        # lowercasing the suffix and this helper not, a ``<id>.YML`` overlay was
+        # ACTIVE during resolution yet reported "not found" by overlay
+        # enable / disable / remove -- applied, but impossible to manage.
+        if not path.is_file() or path.suffix.lower() not in (".yml", ".yaml"):
             continue
         if path.is_symlink():
             continue

tests/specify_cli/workflows/overlay/test_command_disable.py

@@ -4,6 +4,7 @@
 
 from pathlib import Path
 
+import pytest
 import yaml
 from typer.testing import CliRunner
 
@@ -163,3 +164,47 @@ def test_enable_disable_with_mismatched_filename(self, project_dir, monkeypatch)
             )
         )
         assert data["enabled"] is True
+
+
+class TestOverlayUppercaseExtension:
+    """``disable`` must find every overlay the resolver applies.
+
+    ``ProjectOverlaySource.collect`` matches ``.yml``/``.yaml`` case-insensitively,
+    so a ``lint.YML`` overlay is ACTIVE during resolution. ``_find_overlay_file``
+    matched the suffix case-sensitively, so ``disable`` reported that same overlay
+    "not found" -- applied, but impossible to switch off.
+    """
+
+    @pytest.mark.parametrize("filename", ["lint.YML", "lint.Yaml"])
+    def test_disable_finds_uppercase_extension_overlay(
+        self, project_dir, monkeypatch, filename
+    ):
+        monkeypatch.setattr("specify_cli._require_specify_project", lambda: project_dir)
+        _write_workflow(
+            project_dir,
+            "wf",
+            {
+                "schema_version": "1.0",
+                "workflow": {"id": "wf", "name": "WF", "version": "1.0.0"},
+                "steps": [{"id": "a", "type": "command", "command": "echo"}],
+            },
+        )
+        ov_dir = project_dir / ".specify" / "workflows" / "overlays" / "wf"
+        ov_dir.mkdir(parents=True, exist_ok=True)
+        overlay = ov_dir / filename
+        overlay.write_text(
+            yaml.safe_dump(
+                {
+                    "id": "lint",
+                    "extends": "wf",
+                    "priority": 10,
+                    "edits": [{"remove": "a"}],
+                }
+            ),
+            encoding="utf-8",
+        )
+
+        result = runner.invoke(app, ["workflow", "overlay", "disable", "wf", "lint"])
+
+        assert result.exit_code == 0, result.output
+        assert yaml.safe_load(overlay.read_text(encoding="utf-8"))["enabled"] is False

tests/specify_cli/workflows/overlay/test_command_enable.py

@@ -2,7 +2,8 @@
 
 from __future__ import annotations
 
-
+import pytest
+import yaml
 from typer.testing import CliRunner
 
 from specify_cli import app
@@ -30,3 +31,48 @@ def test_overlay_enable_rejects_traversal(self, project_dir, monkeypatch):
         result = runner.invoke(app, ["workflow", "overlay", "enable", "wf", "../other"])
         assert result.exit_code != 0, result.output
         assert "invalid" in result.output.lower() or "traversal" in result.output.lower()
+
+
+class TestOverlayUppercaseExtension:
+    """``enable`` must find every overlay the resolver applies.
+
+    ``ProjectOverlaySource.collect`` matches ``.yml``/``.yaml`` case-insensitively,
+    so a ``lint.YML`` overlay is ACTIVE during resolution. ``_find_overlay_file``
+    matched the suffix case-sensitively, so ``enable`` reported that same overlay
+    "not found" -- disabled, and impossible to switch back on.
+    """
+
+    @pytest.mark.parametrize("filename", ["lint.YML", "lint.Yaml"])
+    def test_enable_finds_uppercase_extension_overlay(
+        self, project_dir, monkeypatch, filename
+    ):
+        monkeypatch.setattr("specify_cli._require_specify_project", lambda: project_dir)
+        _write_workflow(
+            project_dir,
+            "wf",
+            {
+                "schema_version": "1.0",
+                "workflow": {"id": "wf", "name": "WF", "version": "1.0.0"},
+                "steps": [{"id": "a", "type": "command", "command": "echo"}],
+            },
+        )
+        ov_dir = project_dir / ".specify" / "workflows" / "overlays" / "wf"
+        ov_dir.mkdir(parents=True, exist_ok=True)
+        overlay = ov_dir / filename
+        overlay.write_text(
+            yaml.safe_dump(
+                {
+                    "id": "lint",
+                    "extends": "wf",
+                    "priority": 10,
+                    "enabled": False,
+                    "edits": [{"remove": "a"}],
+                }
+            ),
+            encoding="utf-8",
+        )
+
+        result = runner.invoke(app, ["workflow", "overlay", "enable", "wf", "lint"])
+
+        assert result.exit_code == 0, result.output
+        assert yaml.safe_load(overlay.read_text(encoding="utf-8"))["enabled"] is True

tests/specify_cli/workflows/overlay/test_command_remove.py

@@ -4,6 +4,7 @@
 
 from pathlib import Path
 
+import pytest
 import yaml
 from typer.testing import CliRunner
 
@@ -170,3 +171,47 @@ def test_overlay_remove_rejects_symlink(self, project_dir, monkeypatch):
         assert result.exit_code != 0, result.output
         assert real_file.is_file()
         assert "symlink" in result.output.lower() or "Invalid" in result.output
+
+
+class TestOverlayUppercaseExtension:
+    """``remove`` must find every overlay the resolver applies.
+
+    ``ProjectOverlaySource.collect`` matches ``.yml``/``.yaml`` case-insensitively,
+    so a ``lint.YML`` overlay is ACTIVE during resolution. ``_find_overlay_file``
+    matched the suffix case-sensitively, so ``remove`` reported that same overlay
+    "not found" -- applied, but impossible to uninstall.
+    """
+
+    @pytest.mark.parametrize("filename", ["lint.YML", "lint.Yaml"])
+    def test_remove_finds_uppercase_extension_overlay(
+        self, project_dir, monkeypatch, filename
+    ):
+        monkeypatch.setattr("specify_cli._require_specify_project", lambda: project_dir)
+        _write_workflow(
+            project_dir,
+            "wf",
+            {
+                "schema_version": "1.0",
+                "workflow": {"id": "wf", "name": "WF", "version": "1.0.0"},
+                "steps": [{"id": "a", "type": "command", "command": "echo"}],
+            },
+        )
+        ov_dir = project_dir / ".specify" / "workflows" / "overlays" / "wf"
+        ov_dir.mkdir(parents=True, exist_ok=True)
+        overlay = ov_dir / filename
+        overlay.write_text(
+            yaml.safe_dump(
+                {
+                    "id": "lint",
+                    "extends": "wf",
+                    "priority": 10,
+                    "edits": [{"remove": "a"}],
+                }
+            ),
+            encoding="utf-8",
+        )
+
+        result = runner.invoke(app, ["workflow", "overlay", "remove", "wf", "lint"])
+
+        assert result.exit_code == 0, result.output
+        assert not overlay.exists()

tests/workflows/test_overlay_layer_sources.py

@@ -85,6 +85,50 @@ def test_empty_document_still_reports_missing_fields(
         )
 
 
+class TestProjectOverlaySourceExtensionMatching:
+    """Overlay file extensions are matched case-insensitively."""
+
+    @pytest.mark.parametrize(
+        "filename", ["upper.YML", "mixed.Yaml", "shouty.YAML", "title.Yml"]
+    )
+    def test_uppercase_extension_is_collected(
+        self, project_dir: Path, filename: str
+    ) -> None:
+        """A hand-placed `<id>.YML` must not be silently ignored.
+
+        `collect` matched `path.suffix` verbatim against `(".yml", ".yaml")`,
+        so an overlay whose extension differed only in case was skipped with
+        nothing reported — the author's overlay simply never applied. Every
+        other YAML discovery path in the package lowercases before matching.
+        """
+        ov_dir = project_dir / ".specify" / "workflows" / "overlays" / "wf"
+        ov_dir.mkdir(parents=True, exist_ok=True)
+        (ov_dir / filename).write_text(
+            yaml.safe_dump(
+                {
+                    "id": "lint",
+                    "extends": "wf",
+                    "priority": 10,
+                    "edits": [{"remove": "a"}],
+                }
+            ),
+            encoding="utf-8",
+        )
+
+        layers = ProjectOverlaySource(project_dir).collect("wf")
+
+        assert [layer.content.id for layer in layers] == ["lint"]
+
+    def test_non_yaml_extensions_are_still_skipped(self, project_dir: Path) -> None:
+        """Broadening case must not broaden which extensions are accepted."""
+        ov_dir = project_dir / ".specify" / "workflows" / "overlays" / "wf"
+        ov_dir.mkdir(parents=True, exist_ok=True)
+        for name in ("notes.txt", "backup.yml.bak", "README.md", "data.json"):
+            (ov_dir / name).write_text("id: lint\n", encoding="utf-8")
+
+        assert ProjectOverlaySource(project_dir).collect("wf") == []
+
+
 class TestProjectOverlaySourceFileReadErrors:
     """File-read errors must be wrapped in OverlayLoadError, not leaked as raw tracebacks."""