fix: isolate per-extension failures so one bad extension can't drop the rest (#2951)

* fix: isolate per-extension failures in register_enabled_extensions_for_agent

The per-extension loop had no error isolation: if registering one enabled
extension raised (e.g. an OSError writing a command file), the loop aborted and
the exception propagated, so every subsequent enabled extension was silently
skipped. Callers wrap the whole call in a single best-effort try/except, so the
wholesale abort surfaced as one warning while the command still exited 0 —
leaving the agent with only a prefix of its extensions.

Wrap the per-extension body in try/except: warn (naming the extension) and
continue, so one bad extension can no longer drop the others. Add a regression
test that forces the first-iterated extension to raise and asserts the rest
still register.

Closes #2950

* fix(extensions): preserve command registry when skills fail

* fix: clarify skill registration warning

src/specify_cli/extensions.py

@@ -1716,37 +1716,73 @@ class ExtensionManager:
                 continue
 
             ext_dir = self.extensions_dir / ext_id
-            updates: Dict[str, Any] = {}
 
-            if agent_config and not skills_mode_active:
-                registered = registrar.register_commands_for_agent(
-                    agent_name, manifest, ext_dir, self.project_root
-                )
-                registered_commands = metadata.get("registered_commands", {})
-                if not isinstance(registered_commands, dict):
-                    registered_commands = {}
-                new_registered = copy.deepcopy(registered_commands)
-                if registered:
-                    new_registered[agent_name] = registered
+            # Isolate per-extension failures: one extension that fails to
+            # register (e.g. an OSError writing a command file) must not abort
+            # registration of the remaining enabled extensions for this agent.
+            try:
+                updates: Dict[str, Any] = {}
+
+                if agent_config and not skills_mode_active:
+                    registered = registrar.register_commands_for_agent(
+                        agent_name, manifest, ext_dir, self.project_root
+                    )
+                    registered_commands = metadata.get("registered_commands", {})
+                    if not isinstance(registered_commands, dict):
+                        registered_commands = {}
+                    new_registered = copy.deepcopy(registered_commands)
+                    if registered:
+                        new_registered[agent_name] = registered
+                    else:
+                        # Registration returned empty list (e.g., corrupted
+                        # manifest pointing at missing command files).  Clear
+                        # stale entry so later cleanup doesn't try to remove
+                        # files that were never written.
+                        new_registered.pop(agent_name, None)
+                    if new_registered != registered_commands:
+                        updates["registered_commands"] = new_registered
+
+                try:
+                    registered_skills = self._register_extension_skills(manifest, ext_dir)
+                except Exception as skills_err:
+                    # Skills are a companion artifact.  If command registration
+                    # already succeeded, still persist it so later cleanup can
+                    # find those command files.
+                    from . import _print_cli_warning
+
+                    _print_cli_warning(
+                        "register extension skills for",
+                        "extension",
+                        ext_id,
+                        skills_err,
+                        continuing=(
+                            "Continuing with available registration results for this "
+                            "extension and the remaining extensions."
+                        ),
+                    )
                 else:
-                    # Registration returned empty list (e.g., corrupted
-                    # manifest pointing at missing command files).  Clear
-                    # stale entry so later cleanup doesn't try to remove
-                    # files that were never written.
-                    new_registered.pop(agent_name, None)
-                if new_registered != registered_commands:
-                    updates["registered_commands"] = new_registered
+                    if registered_skills:
+                        existing_skills = self._valid_name_list(
+                            metadata.get("registered_skills", [])
+                        )
+                        merged_skills = list(dict.fromkeys(existing_skills + registered_skills))
+                        updates["registered_skills"] = merged_skills
 
-            registered_skills = self._register_extension_skills(manifest, ext_dir)
-            if registered_skills:
-                existing_skills = self._valid_name_list(
-                    metadata.get("registered_skills", [])
+                if updates:
+                    self.registry.update(ext_id, updates)
+            except Exception as ext_err:
+                # Best-effort per extension: warn and move on so a single bad
+                # extension cannot silently drop the others. See #2950.
+                from . import _print_cli_warning
+
+                _print_cli_warning(
+                    "register extension artifacts for",
+                    "extension",
+                    ext_id,
+                    ext_err,
+                    continuing="Continuing with the remaining extensions.",
                 )
-                merged_skills = list(dict.fromkeys(existing_skills + registered_skills))
-                updates["registered_skills"] = merged_skills
-
-            if updates:
-                self.registry.update(ext_id, updates)
+                continue
 
     def list_installed(self) -> List[Dict[str, Any]]:
         """List all installed extensions with metadata.

tests/test_extension_skills.py

@@ -1036,6 +1036,93 @@ class TestExtensionSkillRegistration:
         assert metadata["registered_skills"] == []
         assert (project_dir / ".github" / "agents").is_dir()
 
+    def test_one_failing_extension_does_not_abort_the_rest(
+        self, project_dir, temp_dir, monkeypatch
+    ):
+        """A single failing extension must not block registration of the others.
+
+        Regression for #2950: ``register_enabled_extensions_for_agent`` iterates
+        enabled extensions; before the per-extension isolation, the first one
+        that raised (e.g. an OSError writing a command file) aborted the loop and
+        the exception propagated, so every later extension was silently skipped.
+        """
+        from specify_cli.extensions import CommandRegistrar
+
+        _create_init_options(project_dir, ai="claude", ai_skills=False)
+        manager = ExtensionManager(project_dir)
+        # Two enabled extensions; the first one iterated ("aaa-fail") will raise.
+        manager.install_from_directory(
+            _create_extension_dir(temp_dir, ext_id="aaa-fail"), "0.1.0",
+            register_commands=False,
+        )
+        manager.install_from_directory(
+            _create_extension_dir(temp_dir, ext_id="bbb-ok"), "0.1.0",
+            register_commands=False,
+        )
+
+        original = CommandRegistrar.register_commands_for_agent
+
+        def flaky(self, agent_name, manifest, ext_dir, project_root, link_outputs=False):
+            if manifest.id == "aaa-fail":
+                raise OSError("simulated command-file write failure")
+            return original(
+                self, agent_name, manifest, ext_dir, project_root,
+                link_outputs=link_outputs,
+            )
+
+        monkeypatch.setattr(CommandRegistrar, "register_commands_for_agent", flaky)
+
+        # Must not propagate, despite the first extension failing.
+        manager.register_enabled_extensions_for_agent("claude")
+
+        # The healthy extension was still registered for the agent...
+        ok_meta = manager.registry.get("bbb-ok")
+        assert "claude" in ok_meta["registered_commands"], (
+            "a later extension must still register after an earlier one fails (#2950)"
+        )
+        # ...and the failing one was not.
+        fail_meta = manager.registry.get("aaa-fail")
+        assert "claude" not in fail_meta.get("registered_commands", {})
+
+    def test_skill_registration_failure_preserves_registered_commands(
+        self, project_dir, temp_dir, monkeypatch, capsys
+    ):
+        """Persist successful command registration even if skills fail.
+
+        If command files are written but skill generation raises, the command
+        registry must still be updated so later unregister/cleanup can find the
+        command files.
+        """
+        _create_init_options(project_dir, ai="claude", ai_skills=False)
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(
+            _create_extension_dir(temp_dir, ext_id="skill-fail"), "0.1.0",
+            register_commands=False,
+        )
+
+        def fail_skills(self, manifest, ext_dir, link_outputs=False):
+            raise OSError("simulated skill directory failure")
+
+        monkeypatch.setattr(
+            ExtensionManager, "_register_extension_skills", fail_skills
+        )
+
+        manager.register_enabled_extensions_for_agent("claude")
+
+        metadata = manager.registry.get("skill-fail")
+        assert metadata is not None
+        assert metadata["registered_commands"] == {
+            "claude": [
+                "speckit.skill-fail.hello",
+                "speckit.skill-fail.world",
+            ]
+        }
+        assert metadata["registered_skills"] == []
+
+        captured = capsys.readouterr()
+        assert "register extension skills for extension 'skill-fail'" in captured.out
+        assert "Continuing with available registration results" in captured.out
+
     def test_existing_agent_command_path_file_is_not_detected(
         self, project_dir, temp_dir
     ):