fix(presets): clean up a deleted standalone override's stale script

reconcile_all_script_chains()'s worklist was built from script names
a preset manifest declares plus override files currently on disk. A
deleted standalone override's name drops out of that scan entirely,
so the stale canonical script it left behind survives even an
explicit reconcile call forever -- nothing ever learns the name
needs re-checking again.

Also fold in every name with a provenance sidecar (recorded the last
time this manager generated a canonical script for it), not only
names still declared somewhere today. _reconcile_script_chain()
already restores-to-core or removes a name nothing provides any
more, and already preserves a canonical file the user edited after
the fact via the same provenance hash check -- this just makes sure
a deleted override's name actually reaches that logic again.

Assisted-by: Claude Code (model: Claude Sonnet 5, autonomous)

Author: Ashfaqbs

src/specify_cli/presets/_manager.py

@@ -973,6 +973,19 @@ def reconcile_all_script_chains(self) -> None:
         self-materialize: a project-local override added directly to the
         filesystem outside any lifecycle command still needs this called
         explicitly.
+
+        A *deleted* standalone override is the same situation from the
+        other side: once the override file is gone, scanning the overrides
+        directory alone can never find its name again, so the stale
+        canonical script it left behind -- generated while the override
+        still existed -- would survive even this explicit call forever
+        (#4709 review). Every name with provenance metadata (recorded the
+        last time this manager generated a canonical script for it) is
+        reconciled too, not only names still declared somewhere today;
+        ``_reconcile_script_chain`` already restores-to-core or cleans up
+        a name nothing provides any more, and already preserves a
+        canonical file the user edited after the fact via the same
+        provenance hash check.
         """
         script_names: Set[str] = set()
         for pack_id, _metadata in self.registry.list_by_priority():
@@ -994,6 +1007,12 @@ def reconcile_all_script_chains(self) -> None:
                 override_file.stem
                 for override_file in overrides_scripts_dir.glob("*.sh")
             )
+        scripts_dir = self.project_root / ".specify" / "scripts" / "bash"
+        if scripts_dir.is_dir():
+            script_names.update(
+                provenance_file.name[: -len(_SCRIPT_PROVENANCE_SUFFIX)]
+                for provenance_file in scripts_dir.glob(f"*{_SCRIPT_PROVENANCE_SUFFIX}")
+            )
         for script_name in script_names:
             try:
                 self._reconcile_script_chain(script_name)

tests/specify_cli/presets/test_manager.py

@@ -2089,6 +2089,36 @@ def test_reconcile_all_script_chains_covers_standalone_override(
         chain = PresetResolver(project_dir).resolve_script_chain("setup-plan")
         assert [p.read_text() for p in chain] == ["echo overridden\n"]
 
+    def test_reconcile_all_script_chains_cleans_up_deleted_standalone_override(
+        self, project_dir
+    ):
+        """A deleted standalone override's script name drops out of the
+        overrides-directory scan entirely, so scanning that directory alone
+        can never find it again to clean up the stale canonical script it
+        left behind -- even on an explicit reconcile_all_script_chains()
+        call (#4709 review). Provenance metadata recorded when this manager
+        generated the canonical script must be consulted too, not just
+        names still declared somewhere today."""
+        override_dir = (
+            project_dir / ".specify" / "templates" / "overrides" / "scripts"
+        )
+        override_dir.mkdir(parents=True, exist_ok=True)
+        (override_dir / "deleted-override-script.sh").write_text("echo overridden\n")
+
+        manager = PresetManager(project_dir)
+        manager.reconcile_all_script_chains()
+
+        canonical = self._canonical(project_dir, "deleted-override-script")
+        assert canonical.read_text() == "echo overridden\n"
+
+        (override_dir / "deleted-override-script.sh").unlink()
+        manager.reconcile_all_script_chains()
+
+        # No core/bundled fallback exists for this name either, so the
+        # stale canonical file (and its provenance sidecar) must be
+        # removed entirely, not merely left with its old content.
+        assert not canonical.exists()
+
     def test_enable_disable_and_set_priority_rematerialize_scripts(
         self, project_dir, temp_dir, valid_pack_data
     ):