Verify replacement actually landed before retiring stale toggle artifacts

The command<->skills toggle cleanup added for #2948 deferred destructive
removal of the old-mode artifact until after the replacement registration
call completed without raising. That was necessary but not sufficient:
none of _register_skills(), _register_commands(),
register_commands_for_agent(), or _register_extension_skills() raise on
a missing source template, a safety-validation skip, or a corrupted
manifest entry — they simply return an empty or partial result. Treating
"did not raise" as "fully replaced" meant a stale artifact could still be
deleted (or its tracking dropped) even though its specific replacement
never actually landed, leaving neither artifact in place for that logical
command/skill.

Fix all four affected toggle directions by checking the replacement
call's actual return value before allowing any destructive step:

- presets command->skills (register_enabled_presets_for_agent): only
  unregister a stale command name once its corresponding skill name
  (via the existing _skill_names_for_command() helper) is confirmed
  present in the skills call's returned names for that agent; the
  remainder stays tracked and on disk.
- presets skills->command (register_enabled_presets_for_agent): only
  unregister a stale skill name once its corresponding command name is
  confirmed present in the commands call's returned names for that
  agent, using the same helper.
- extensions skills->command (register_enabled_extensions_for_agent):
  only remove a skill mirror once the matching command (mapped via the
  existing HookExecutor._skill_name_from_command() helper) is confirmed
  present in register_commands_for_agent's returned names.
- extensions command->skills (register_enabled_extensions_for_agent):
  only remove a deferred stale command once its matching skill name is
  confirmed present in _register_extension_skills()'s returned names.

All four reuse the existing command<->skill name-derivation helpers
rather than inventing new mapping logic. Registry tracking is updated to
retain exactly the unreplaced subset rather than being popped wholesale,
so partially-successful toggles leave correct, minimal tracking behind.

Added 8 new regression tests (4 presets, 4 extensions) covering both the
fully-empty and genuinely-partial result cases for each of the four
toggle directions, using real missing-source-file scenarios (not mocked
return values) to exercise the actual code paths. Confirmed red before
the fix and green after for all 8.

Focused (test_presets.py, test_extension_skills.py, test_extensions.py,
tests/integrations): 2551 passed, 1 skipped.
Full suite (tests, excluding the pre-existing environment-local
1Password-signing git-extension failures): 3917 passed, 74 skipped, 90
deselected.
ruff check: clean.

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/specify_cli/extensions/__init__.py

@@ -2103,9 +2103,26 @@ class ExtensionManager:
                                 for name in existing_skills
                                 if (agent_skills_dir / name).is_dir()
                             ]
-                            if owned_here:
+                            # Only retire a skill mirror when the
+                            # replacement command for the same logical
+                            # command was actually written this call —
+                            # `registered` (from register_commands_for_agent
+                            # above) may be empty or a partial subset
+                            # (missing source file, safety rejection,
+                            # corrupted manifest), and removing a skill
+                            # mirror whose command replacement never
+                            # landed would leave neither artifact (#2948).
+                            replaced_skill_names = {
+                                HookExecutor._skill_name_from_command(cmd_name)
+                                for cmd_name in (registered or [])
+                            }
+                            to_remove = [
+                                name for name in owned_here
+                                if name in replaced_skill_names
+                            ]
+                            if to_remove:
                                 self._unregister_extension_skills(
-                                    owned_here, ext_id, skills_dir=agent_skills_dir
+                                    to_remove, ext_id, skills_dir=agent_skills_dir
                                 )
                                 # registered_skills is a single flat list
                                 # shared across every agent this extension
@@ -2132,17 +2149,41 @@ class ExtensionManager:
                         # registration is confirmed, so the stale
                         # command-mode artifact can finally be removed
                         # without risking a transient state where neither
-                        # artifact exists (#2948).
+                        # artifact exists. Only retire a stale command
+                        # whose corresponding skill was actually returned
+                        # this call — `registered_skills` may be empty or
+                        # a partial subset (missing source file, safety
+                        # rejection, corrupted manifest), and unregistering
+                        # a command whose skill replacement never landed
+                        # would leave neither artifact (#2948).
                         if deferred_stale_commands:
-                            registrar.unregister_commands(
-                                {agent_name: deferred_stale_commands}, self.project_root
-                            )
-                            registered_commands = metadata.get("registered_commands", {})
-                            if isinstance(registered_commands, dict):
-                                new_registered = copy.deepcopy(registered_commands)
-                                new_registered.pop(agent_name, None)
-                                if new_registered != registered_commands:
-                                    updates["registered_commands"] = new_registered
+                            replaced_skill_names = set(registered_skills or [])
+                            fully_replaced = [
+                                cmd_name for cmd_name in deferred_stale_commands
+                                if HookExecutor._skill_name_from_command(cmd_name)
+                                in replaced_skill_names
+                            ]
+                            if fully_replaced:
+                                registrar.unregister_commands(
+                                    {agent_name: fully_replaced}, self.project_root
+                                )
+                                registered_commands = metadata.get(
+                                    "registered_commands", {}
+                                )
+                                if isinstance(registered_commands, dict) and (
+                                    registered_commands.get(agent_name)
+                                ):
+                                    new_registered = copy.deepcopy(registered_commands)
+                                    remaining_commands = [
+                                        c for c in new_registered[agent_name]
+                                        if c not in fully_replaced
+                                    ]
+                                    if remaining_commands:
+                                        new_registered[agent_name] = remaining_commands
+                                    else:
+                                        new_registered.pop(agent_name, None)
+                                    if new_registered != registered_commands:
+                                        updates["registered_commands"] = new_registered
 
                 if updates:
                     self.registry.update(ext_id, updates)

src/specify_cli/presets/__init__.py

@@ -854,11 +854,28 @@ class PresetManager:
                     # direction is already register-new-then-remove-old:
                     # _register_commands (the replacement) ran unconditionally
                     # above and only reaches here once it has already
-                    # succeeded, so this cleanup happens only after the new
-                    # command artifact is confirmed in place (#2948).
-                    self._unregister_skills(
-                        {agent_name: merged_skills.pop(agent_name)}, pack_dir
-                    )
+                    # succeeded — but that call can still have returned
+                    # empty or partial results (missing source template,
+                    # safety-validation skip, corrupted manifest), so only
+                    # retire the subset of stale skills whose corresponding
+                    # command name was actually returned for this agent;
+                    # anything unreplaced stays tracked and on disk (#2948).
+                    stale_skill_names = merged_skills[agent_name]
+                    replaced_skill_names: set = set()
+                    for cmd_name in registered_commands.get(agent_name) or []:
+                        modern_name, legacy_name = self._skill_names_for_command(cmd_name)
+                        replaced_skill_names.add(modern_name)
+                        replaced_skill_names.add(legacy_name)
+                    to_remove = [n for n in stale_skill_names if n in replaced_skill_names]
+                    remaining_stale = [
+                        n for n in stale_skill_names if n not in replaced_skill_names
+                    ]
+                    if to_remove:
+                        self._unregister_skills({agent_name: to_remove}, pack_dir)
+                    if remaining_stale:
+                        merged_skills[agent_name] = remaining_stale
+                    else:
+                        merged_skills.pop(agent_name, None)
                 # A legacy flat-list registered_skills value (predating
                 # per-agent provenance) must migrate to the dict format on
                 # disk even when the rescaffolded names are unchanged from
@@ -874,14 +891,32 @@ class PresetManager:
                 if merged_skills != existing_skills or needs_migration:
                     self.registry.update(pack_id, {"registered_skills": merged_skills})
 
-                # The skills phase above completed without raising, so the
-                # replacement artifact is confirmed — now it's safe to
-                # remove the stale command-mode artifact deferred earlier
-                # (#2948).
+                # The skills phase above completed without raising, but a
+                # non-raising result can still be empty or partial (missing
+                # source template, safety-validation skip, corrupted
+                # manifest) — retiring every stale command purely on "did
+                # not raise" would delete a command whose replacement skill
+                # never actually landed, leaving neither artifact. Only
+                # retire the subset of stale commands whose corresponding
+                # skill name was actually returned for this agent; anything
+                # unreplaced stays tracked and on disk (#2948).
                 if stale_command_names:
-                    self._unregister_commands({agent_name: stale_command_names})
-                    merged_commands.pop(agent_name, None)
-                    self.registry.update(pack_id, {"registered_commands": merged_commands})
+                    replaced_skill_names = set(registered_skills.get(agent_name) or [])
+                    fully_replaced = []
+                    remaining_stale = []
+                    for cmd_name in stale_command_names:
+                        modern_name, legacy_name = self._skill_names_for_command(cmd_name)
+                        if modern_name in replaced_skill_names or legacy_name in replaced_skill_names:
+                            fully_replaced.append(cmd_name)
+                        else:
+                            remaining_stale.append(cmd_name)
+                    if fully_replaced:
+                        self._unregister_commands({agent_name: fully_replaced})
+                        if remaining_stale:
+                            merged_commands[agent_name] = remaining_stale
+                        else:
+                            merged_commands.pop(agent_name, None)
+                        self.registry.update(pack_id, {"registered_commands": merged_commands})
             except Exception as pack_err:
                 from .. import _print_cli_warning
 

tests/test_extension_skills.py

@@ -1366,6 +1366,221 @@ class TestExtensionSkillRegistration:
             "command file when the skills replacement failed (#2948)"
         )
 
+    def test_toggle_command_to_skills_empty_result_preserves_old_extension_command(
+        self, project_dir, temp_dir
+    ):
+        """An empty (non-raising) skills result must not delete any old
+        extension command artifact.
+
+        Deleting both of the extension's own installed command source
+        files makes ``_register_extension_skills`` genuinely return ``[]``
+        for copilot without raising — a real "missing source" case, not an
+        injected exception — which must leave both old command-mode
+        artifacts and their tracking untouched (#2948).
+        """
+        _create_init_options(project_dir, ai="copilot", ai_skills=False)
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(
+            _create_extension_dir(temp_dir, ext_id="toggle-empty-ext"), "0.1.0",
+            register_commands=False,
+        )
+        manager.register_enabled_extensions_for_agent("copilot")
+
+        agents_dir = project_dir / ".github" / "agents"
+        hello_cmd_file = agents_dir / "speckit.toggle-empty-ext.hello.agent.md"
+        world_cmd_file = agents_dir / "speckit.toggle-empty-ext.world.agent.md"
+        assert hello_cmd_file.exists() and world_cmd_file.exists(), (
+            "sanity: command mode should have written both command files"
+        )
+
+        # Remove both installed command sources so _register_extension_skills
+        # can find nothing to render for either command.
+        ext_commands_dir = manager.extensions_dir / "toggle-empty-ext" / "commands"
+        (ext_commands_dir / "hello.md").unlink()
+        (ext_commands_dir / "world.md").unlink()
+
+        _create_init_options(project_dir, ai="copilot", ai_skills=True)
+        manager.register_enabled_extensions_for_agent("copilot")
+
+        assert hello_cmd_file.exists() and world_cmd_file.exists(), (
+            "an empty (non-raising) skills registration result must not "
+            "cause the old command-mode artifacts to be deleted (#2948)"
+        )
+        metadata = manager.registry.get("toggle-empty-ext")
+        registered_commands = metadata.get("registered_commands", {}).get("copilot", [])
+        assert set(registered_commands) == {
+            "speckit.toggle-empty-ext.hello", "speckit.toggle-empty-ext.world",
+        }, (
+            "registered_commands must keep tracking copilot's still-live "
+            "command files when nothing was actually replaced (#2948)"
+        )
+        skills_dir = project_dir / ".github" / "skills"
+        assert not (skills_dir / "speckit-toggle-empty-ext-hello").exists(), (
+            "sanity: no skill should have been written when both sources "
+            "were missing"
+        )
+        assert not (skills_dir / "speckit-toggle-empty-ext-world").exists()
+
+    def test_toggle_command_to_skills_partial_result_only_removes_replaced_extension_command(
+        self, project_dir, temp_dir
+    ):
+        """Only the extension command whose skill replacement actually
+        landed is retired.
+
+        A two-command extension (hello, world) where only ``world``'s
+        installed source goes missing right before the toggle, so
+        ``_register_extension_skills`` genuinely returns a partial result
+        (only ``hello``'s skill). ``hello``'s old command artifact must be
+        retired; ``world``'s must survive with its tracking intact, since
+        no replacement for it landed (#2948).
+        """
+        _create_init_options(project_dir, ai="copilot", ai_skills=False)
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(
+            _create_extension_dir(temp_dir, ext_id="toggle-partial-ext"), "0.1.0",
+            register_commands=False,
+        )
+        manager.register_enabled_extensions_for_agent("copilot")
+
+        agents_dir = project_dir / ".github" / "agents"
+        hello_cmd_file = agents_dir / "speckit.toggle-partial-ext.hello.agent.md"
+        world_cmd_file = agents_dir / "speckit.toggle-partial-ext.world.agent.md"
+        assert hello_cmd_file.exists() and world_cmd_file.exists(), (
+            "sanity: command mode should have written both command files"
+        )
+
+        # Remove only world's installed source so its skill replacement is
+        # silently skipped (missing source), while hello's succeeds.
+        ext_commands_dir = manager.extensions_dir / "toggle-partial-ext" / "commands"
+        (ext_commands_dir / "world.md").unlink()
+
+        _create_init_options(project_dir, ai="copilot", ai_skills=True)
+        manager.register_enabled_extensions_for_agent("copilot")
+
+        assert not hello_cmd_file.exists(), (
+            "hello's old command artifact must be retired since its skill "
+            "replacement actually landed (#2948)"
+        )
+        assert world_cmd_file.exists(), (
+            "world's old command artifact must survive since its skill "
+            "replacement never landed (missing source) (#2948)"
+        )
+        metadata = manager.registry.get("toggle-partial-ext")
+        registered_commands = metadata.get("registered_commands", {}).get("copilot", [])
+        assert registered_commands == ["speckit.toggle-partial-ext.world"], (
+            "registered_commands must stop tracking hello (retired) but "
+            "keep tracking world (still live) (#2948)"
+        )
+        skills_dir = project_dir / ".github" / "skills"
+        assert (skills_dir / "speckit-toggle-partial-ext-hello" / "SKILL.md").exists()
+        assert not (skills_dir / "speckit-toggle-partial-ext-world").exists()
+
+    def test_toggle_skills_to_command_empty_result_preserves_old_extension_skill(
+        self, project_dir, temp_dir
+    ):
+        """An empty (non-raising) command result must not delete any old
+        extension skill artifact.
+
+        Mirror image of the empty-result command->skills case: deleting
+        both of the extension's own installed command source files makes
+        ``register_commands_for_agent`` genuinely return an empty/falsy
+        result for copilot without raising, which must leave both old
+        skill-mode artifacts and their tracking untouched (#2948).
+        """
+        _create_init_options(project_dir, ai="copilot", ai_skills=True)
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(
+            _create_extension_dir(temp_dir, ext_id="toggle-skill-empty-ext"), "0.1.0",
+            register_commands=False,
+        )
+        manager.register_enabled_extensions_for_agent("copilot")
+
+        skills_dir = project_dir / ".github" / "skills"
+        hello_skill_file = skills_dir / "speckit-toggle-skill-empty-ext-hello" / "SKILL.md"
+        world_skill_file = skills_dir / "speckit-toggle-skill-empty-ext-world" / "SKILL.md"
+        assert hello_skill_file.exists() and world_skill_file.exists(), (
+            "sanity: skills mode should have written both SKILL.md mirrors"
+        )
+
+        # Remove both installed command sources so register_commands_for_agent
+        # can find nothing to render for either command.
+        ext_commands_dir = manager.extensions_dir / "toggle-skill-empty-ext" / "commands"
+        (ext_commands_dir / "hello.md").unlink()
+        (ext_commands_dir / "world.md").unlink()
+
+        _create_init_options(project_dir, ai="copilot", ai_skills=False)
+        manager.register_enabled_extensions_for_agent("copilot")
+
+        assert hello_skill_file.exists() and world_skill_file.exists(), (
+            "an empty (non-raising) command registration result must not "
+            "cause the old skills-mode artifacts to be deleted (#2948)"
+        )
+        metadata = manager.registry.get("toggle-skill-empty-ext")
+        registered_skills = metadata.get("registered_skills", [])
+        assert {
+            "speckit-toggle-skill-empty-ext-hello",
+            "speckit-toggle-skill-empty-ext-world",
+        } <= set(registered_skills), (
+            "registered_skills must keep tracking copilot's still-live "
+            "skill files when nothing was actually replaced (#2948)"
+        )
+
+    def test_toggle_skills_to_command_partial_result_only_removes_replaced_extension_skill(
+        self, project_dir, temp_dir
+    ):
+        """Only the extension skill whose command replacement actually
+        landed is retired.
+
+        Mirror image of the partial-result command->skills case: a
+        two-command extension where only ``world``'s installed source goes
+        missing right before the toggle, so ``register_commands_for_agent``
+        genuinely returns a partial result (only ``hello``'s command).
+        ``hello``'s old skill artifact must be retired; ``world``'s must
+        survive with its tracking intact, since no replacement for it
+        landed (#2948).
+        """
+        _create_init_options(project_dir, ai="copilot", ai_skills=True)
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(
+            _create_extension_dir(temp_dir, ext_id="toggle-skill-partial-ext"), "0.1.0",
+            register_commands=False,
+        )
+        manager.register_enabled_extensions_for_agent("copilot")
+
+        skills_dir = project_dir / ".github" / "skills"
+        hello_skill_file = skills_dir / "speckit-toggle-skill-partial-ext-hello" / "SKILL.md"
+        world_skill_file = skills_dir / "speckit-toggle-skill-partial-ext-world" / "SKILL.md"
+        assert hello_skill_file.exists() and world_skill_file.exists(), (
+            "sanity: skills mode should have written both SKILL.md mirrors"
+        )
+
+        # Remove only world's installed source so its command replacement
+        # is silently skipped (missing source), while hello's succeeds.
+        ext_commands_dir = manager.extensions_dir / "toggle-skill-partial-ext" / "commands"
+        (ext_commands_dir / "world.md").unlink()
+
+        _create_init_options(project_dir, ai="copilot", ai_skills=False)
+        manager.register_enabled_extensions_for_agent("copilot")
+
+        assert not hello_skill_file.exists(), (
+            "hello's old skill artifact must be retired since its command "
+            "replacement actually landed (#2948)"
+        )
+        assert world_skill_file.exists(), (
+            "world's old skill artifact must survive since its command "
+            "replacement never landed (missing source) (#2948)"
+        )
+        metadata = manager.registry.get("toggle-skill-partial-ext")
+        registered_skills = metadata.get("registered_skills", [])
+        assert "speckit-toggle-skill-partial-ext-hello" not in registered_skills, (
+            "hello must stop being tracked as a skill once its artifact "
+            "has been unregistered (#2948)"
+        )
+        assert "speckit-toggle-skill-partial-ext-world" in registered_skills, (
+            "world must keep being tracked as a skill since its old "
+            "artifact is still on disk (#2948)"
+        )
+
     def test_rescaffold_toggle_skills_to_command_removes_stale_extension_skill_file(
         self, project_dir, temp_dir
     ):

tests/test_presets.py

@@ -3186,6 +3186,44 @@ class TestPresetSkills:
             yaml.dump(manifest_data, f)
         return preset_dir
 
+    def _create_multi_command_preset(self, temp_dir, preset_id, command_names):
+        """Install-directory helper for a preset with more than one command.
+
+        Used to prove partial-result handling: a command's own template
+        entry can genuinely be skipped by registration (missing source
+        file, safety-validation rejection) while sibling commands in the
+        same preset still succeed.
+        """
+        preset_dir = temp_dir / preset_id
+        preset_dir.mkdir()
+        (preset_dir / "commands").mkdir()
+        templates = []
+        for command_name in command_names:
+            command_file = f"{command_name}.md"
+            (preset_dir / "commands" / command_file).write_text(
+                f"---\ndescription: {command_name} test command\n---\n\n"
+                f"{command_name} body\n"
+            )
+            templates.append({
+                "type": "command",
+                "name": command_name,
+                "file": f"commands/{command_file}",
+            })
+        manifest_data = {
+            "schema_version": "1.0",
+            "preset": {
+                "id": preset_id,
+                "name": preset_id,
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {"templates": templates},
+        }
+        with open(preset_dir / "preset.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+        return preset_dir
+
     def test_skill_overridden_on_preset_install(self, project_dir, temp_dir):
         """When skills mode was used, a preset command override should update the skill."""
         # Simulate skills mode having been used: write init-options + create skill
@@ -4486,6 +4524,260 @@ class TestPresetSkills:
             "even though the file is still on disk (#2948)"
         )
 
+    def test_toggle_command_to_skills_empty_result_preserves_old_command(
+        self, project_dir, temp_dir
+    ):
+        """A non-raising but empty skills result must not delete the old command.
+
+        Before the fix, the stale command-mode artifact was retired as
+        soon as ``_register_skills()`` completed without raising —
+        regardless of whether it actually wrote anything for this agent.
+        Deleting the preset's own command source file (simulating a
+        missing/corrupted override) makes ``_register_skills`` return
+        ``{}`` for copilot without raising at all, which must leave the
+        old command file and its tracking untouched (#2948).
+        """
+        self._write_init_options(project_dir, ai="copilot", ai_skills=False)
+        copilot_commands_dir = project_dir / ".github" / "agents"
+        copilot_commands_dir.mkdir(parents=True)
+
+        preset_dir = self._create_command_preset(
+            temp_dir, "toggle-empty-result-preset", "speckit.specify",
+            "Toggle empty-result test", "preset body",
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        cmd_file = copilot_commands_dir / "speckit.specify.agent.md"
+        assert cmd_file.exists(), (
+            "sanity: command mode should have written copilot's command file"
+        )
+
+        # Remove the *installed* copy of the preset's source file (not the
+        # original temp source) so _register_skills can find nothing to
+        # render — a real "missing source" case, not an exception — leaving
+        # registered_skills empty for copilot.
+        (manager.presets_dir / "toggle-empty-result-preset" / "commands" / "speckit.specify.md").unlink()
+
+        self._write_init_options(project_dir, ai="copilot", ai_skills=True)
+        manager.register_enabled_presets_for_agent("copilot")
+
+        assert cmd_file.exists(), (
+            "an empty (non-raising) skills registration result must not "
+            "cause the old command-mode artifact to be deleted (#2948)"
+        )
+        metadata = manager.registry.get("toggle-empty-result-preset")
+        assert metadata["registered_commands"].get("copilot"), (
+            "registered_commands must keep tracking copilot's still-live "
+            "command file when nothing was actually replaced (#2948)"
+        )
+        skill_file = project_dir / ".github" / "skills" / "speckit-specify" / "SKILL.md"
+        assert not skill_file.exists(), (
+            "sanity: no skill should have been written when the source "
+            "was missing"
+        )
+
+    def test_toggle_command_to_skills_partial_result_only_removes_replaced_command(
+        self, project_dir, temp_dir
+    ):
+        """Only the command whose skill replacement actually landed is retired.
+
+        A two-command preset where one command's source file goes missing
+        right before the toggle: ``_register_skills`` genuinely returns a
+        partial result (one name present, one silently skipped) without
+        raising. The command whose skill was written must be retired; the
+        other must keep both its old command file and its registry
+        tracking, since no replacement for it actually landed (#2948).
+        """
+        self._write_init_options(project_dir, ai="copilot", ai_skills=False)
+        copilot_commands_dir = project_dir / ".github" / "agents"
+        copilot_commands_dir.mkdir(parents=True)
+
+        preset_dir = self._create_multi_command_preset(
+            temp_dir, "toggle-partial-result-preset",
+            ["speckit.specify", "speckit.plan"],
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        specify_cmd_file = copilot_commands_dir / "speckit.specify.agent.md"
+        plan_cmd_file = copilot_commands_dir / "speckit.plan.agent.md"
+        assert specify_cmd_file.exists() and plan_cmd_file.exists(), (
+            "sanity: command mode should have written both command files"
+        )
+        metadata = manager.registry.get("toggle-partial-result-preset")
+        assert set(metadata["registered_commands"].get("copilot", [])) == {
+            "speckit.specify", "speckit.plan",
+        }, "sanity: both commands should be tracked for copilot"
+
+        # Remove only the plan command's *installed* source so its skill
+        # replacement is silently skipped (missing source), while
+        # specify's succeeds — a genuine partial result, not an injected
+        # exception.
+        (manager.presets_dir / "toggle-partial-result-preset" / "commands" / "speckit.plan.md").unlink()
+
+        self._write_init_options(project_dir, ai="copilot", ai_skills=True)
+        manager.register_enabled_presets_for_agent("copilot")
+
+        assert not specify_cmd_file.exists(), (
+            "the specify command's old artifact must be retired since its "
+            "skill replacement actually landed (#2948)"
+        )
+        assert plan_cmd_file.exists(), (
+            "the plan command's old artifact must survive since its skill "
+            "replacement never landed (missing source) (#2948)"
+        )
+        metadata = manager.registry.get("toggle-partial-result-preset")
+        tracked_commands = metadata["registered_commands"].get("copilot", [])
+        assert "speckit.specify" not in tracked_commands, (
+            "specify must stop being tracked as a command once its "
+            "artifact has been unregistered (#2948)"
+        )
+        assert "speckit.plan" in tracked_commands, (
+            "plan must keep being tracked as a command since its old "
+            "artifact is still on disk (#2948)"
+        )
+        specify_skill_file = (
+            project_dir / ".github" / "skills" / "speckit-specify" / "SKILL.md"
+        )
+        assert "preset:toggle-partial-result-preset" in specify_skill_file.read_text(), (
+            "sanity: specify's new skill artifact should exist"
+        )
+        plan_skill_file = project_dir / ".github" / "skills" / "speckit-plan"
+        assert not plan_skill_file.exists(), (
+            "sanity: no skill should have been written for plan since its "
+            "source was missing"
+        )
+
+    def test_toggle_skills_to_command_empty_result_preserves_old_skill(
+        self, project_dir, temp_dir
+    ):
+        """A non-raising but empty command result must not delete the old skill.
+
+        Mirror image of the empty-result command->skills case: deleting the
+        preset's own source file makes ``_register_commands`` return ``{}``
+        for copilot without raising, which must leave the old SKILL.md and
+        its tracking untouched (#2948).
+        """
+        self._write_init_options(project_dir, ai="copilot", ai_skills=True)
+        copilot_commands_dir = project_dir / ".github" / "agents"
+        copilot_commands_dir.mkdir(parents=True)
+        skills_dir = project_dir / ".github" / "skills"
+        self._create_skill(skills_dir, "speckit-specify")
+
+        preset_dir = self._create_command_preset(
+            temp_dir, "toggle-skill-empty-result-preset", "speckit.specify",
+            "Toggle empty-result test", "preset body",
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        skill_file = skills_dir / "speckit-specify" / "SKILL.md"
+        assert "preset:toggle-skill-empty-result-preset" in skill_file.read_text(), (
+            "sanity: skills mode should have written the SKILL.md mirror"
+        )
+
+        # Remove the preset's own *installed* source file so
+        # _register_commands can find nothing to render — a real "missing
+        # source" case, not an exception — leaving registered_commands
+        # empty for copilot.
+        (manager.presets_dir / "toggle-skill-empty-result-preset" / "commands" / "speckit.specify.md").unlink()
+
+        self._write_init_options(project_dir, ai="copilot", ai_skills=False)
+        manager.register_enabled_presets_for_agent("copilot")
+
+        assert "preset:toggle-skill-empty-result-preset" in skill_file.read_text(), (
+            "an empty (non-raising) command registration result must not "
+            "cause the old skills-mode artifact to be deleted/reverted "
+            "(#2948)"
+        )
+        metadata = manager.registry.get("toggle-skill-empty-result-preset")
+        assert "speckit-specify" in metadata["registered_skills"].get("copilot", []), (
+            "registered_skills must keep tracking copilot's still-live "
+            "skill file when nothing was actually replaced (#2948)"
+        )
+        # Note: a command file may still exist here — general command
+        # reconciliation independently restores the next-best (e.g. core)
+        # layer for the *command name*, regardless of this preset's own
+        # missing source. That's an orthogonal, existing behaviour; the
+        # invariant under test is specifically that the *skill* mirror and
+        # its tracking survive the empty registration result.
+
+    def test_toggle_skills_to_command_partial_result_only_removes_replaced_skill(
+        self, project_dir, temp_dir
+    ):
+        """Only the skill whose command replacement actually landed is retired.
+
+        Mirror image of the partial-result command->skills case: a
+        two-command preset where one command's source file goes missing
+        right before the toggle, so ``_register_commands`` genuinely
+        returns a partial result. The skill whose command was written
+        must be retired; the other must keep both its old SKILL.md and
+        its registry tracking, since no replacement for it landed (#2948).
+        """
+        self._write_init_options(project_dir, ai="copilot", ai_skills=True)
+        copilot_commands_dir = project_dir / ".github" / "agents"
+        copilot_commands_dir.mkdir(parents=True)
+        skills_dir = project_dir / ".github" / "skills"
+        self._create_skill(skills_dir, "speckit-specify")
+        self._create_skill(skills_dir, "speckit-plan")
+
+        # A core template lets the retired skill restore to core content
+        # instead of being removed entirely (it has nothing else to fall
+        # back to), matching _unregister_skills's behaviour elsewhere.
+        core_cmds = project_dir / ".specify" / "templates" / "commands"
+        core_cmds.mkdir(parents=True, exist_ok=True)
+        (core_cmds / "specify.md").write_text(
+            "---\ndescription: Core specify command\n---\n\nCore specify body\n",
+            encoding="utf-8",
+        )
+
+        preset_dir = self._create_multi_command_preset(
+            temp_dir, "toggle-skill-partial-result-preset",
+            ["speckit.specify", "speckit.plan"],
+        )
+        manager = PresetManager(project_dir)
+        manager.install_from_directory(preset_dir, "0.1.5")
+
+        specify_skill_file = skills_dir / "speckit-specify" / "SKILL.md"
+        plan_skill_file = skills_dir / "speckit-plan" / "SKILL.md"
+        assert "preset:toggle-skill-partial-result-preset" in specify_skill_file.read_text()
+        assert "preset:toggle-skill-partial-result-preset" in plan_skill_file.read_text()
+        metadata = manager.registry.get("toggle-skill-partial-result-preset")
+        assert set(metadata["registered_skills"].get("copilot", [])) == {
+            "speckit-specify", "speckit-plan",
+        }, "sanity: both skills should be tracked for copilot"
+
+        # Remove only the plan command's *installed* source so its command
+        # replacement is silently skipped (missing source), while
+        # specify's succeeds.
+        (manager.presets_dir / "toggle-skill-partial-result-preset" / "commands" / "speckit.plan.md").unlink()
+
+        self._write_init_options(project_dir, ai="copilot", ai_skills=False)
+        manager.register_enabled_presets_for_agent("copilot")
+
+        assert "preset:toggle-skill-partial-result-preset" not in specify_skill_file.read_text(), (
+            "the specify skill's old artifact must be retired/reverted "
+            "since its command replacement actually landed (#2948)"
+        )
+        assert "preset:toggle-skill-partial-result-preset" in plan_skill_file.read_text(), (
+            "the plan skill's old artifact must survive since its command "
+            "replacement never landed (missing source) (#2948)"
+        )
+        metadata = manager.registry.get("toggle-skill-partial-result-preset")
+        tracked_skills = metadata["registered_skills"].get("copilot", [])
+        assert "speckit-specify" not in tracked_skills, (
+            "specify must stop being tracked as a skill once its artifact "
+            "has been unregistered/reverted (#2948)"
+        )
+        assert "speckit-plan" in tracked_skills, (
+            "plan must keep being tracked as a skill since its old "
+            "artifact is still on disk (#2948)"
+        )
+        assert (copilot_commands_dir / "speckit.specify.agent.md").exists(), (
+            "sanity: specify's new command artifact should exist"
+        )
+
     def test_rescaffold_toggle_skills_to_command_removes_stale_skill_file(
         self, project_dir, temp_dir
     ):