Fix: scaffold self-contained namespaced preset commands (#4076) (#4082)

* Fix: scaffold self-contained namespaced preset commands (#4076)

Preset command templates named `speckit.<ns>.<cmd>` were silently dropped
whenever `.specify/extensions/<ns>/` was absent, while `speckit.<cmd>`
always scaffolded. The `_extension_installed_for_command` guard filtered
purely on name shape, conflating "override of an installed extension's
command" with "a preset shipping its own namespaced command." Because a
`type: command` template always ships its own body, such a command is
self-contained and must scaffold like any short-named command.

Remove the name-shape guard at all four call sites (registration, both
reconciliation passes, and skills). The reconciliation loop already skips
names that resolve to no layers (`if not layers: continue`), and the
composed-None branch still cleans up commands whose base layer disappeared.
Convert the command-mode "no base layer to compose onto" hard error into a
warn + skip, matching the existing behavior in _reconcile_composed_commands
so command-mode install and reconciliation stay consistent.

Update the two tests that encoded the old drop behavior to assert the new
consistent-scaffold contract, and add coverage proving 2-part and 3-part
preset commands scaffold identically with no extension installed.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)
Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: cfc4f1ce-6acb-465a-aa7b-999f2e4197fb

* Skip uncomposable commands in skills mode too (PR #4082 review)

When _register_commands skips an uncomposable composition command (a
wrap/prepend/append with no base layer to compose onto — e.g. the command
it wraps comes from an uninstalled extension), install still passed the
full manifest to _register_skills. For a command-backed integration in
skills mode, _register_skills created the missing skill and fell back to
the raw preset body because no `.composed` file existed, materializing a
broken SKILL.md — a literal `{CORE_TEMPLATE}` for wrap, or just the
preset's own fragment for prepend/append. Previously the raise in
_register_commands aborted before skills ran, so this never surfaced.

Make _register_skills apply the same skip: for a composition-strategy
command with no `.composed` file, resolve the stack and skip when no base
exists (resolve_content is None). The skip is silent because
_register_commands already warned for the same command in the same pass.

Add a regression test proving an uncomposable wrap command renders no skill
and never leaks a literal {CORE_TEMPLATE} in skills mode.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)
Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: cfc4f1ce-6acb-465a-aa7b-999f2e4197fb

---------

Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: cfc4f1ce-6acb-465a-aa7b-999f2e4197fb

Author: mnriem

src/specify_cli/presets/__init__.py

@@ -823,25 +823,6 @@ def check_compatibility(
 
         return True
 
-    def _extension_installed_for_command(self, command_name: str) -> bool:
-        """Whether *command_name* may be materialized in this project.
-
-        Extension command overrides follow ``speckit.<ext-id>.<cmd-name>``;
-        they must be skipped everywhere preset artifacts are written —
-        registration *and* reconciliation — when the extension isn't
-        installed, or reconciliation would materialize files that
-        registration refused to track. Core commands (single-dot names,
-        e.g. ``speckit.specify``) always pass.
-        """
-        parts = command_name.split(".")
-        if len(parts) >= 3 and parts[0] == "speckit":
-            ext_id = parts[1]
-            if not (
-                self.project_root / ".specify" / "extensions" / ext_id
-            ).is_dir():
-                return False
-        return True
-
     def _register_commands(
         self,
         manifest: PresetManifest,
@@ -870,21 +851,20 @@ def _register_commands(
         if not command_templates:
             return {}
 
-        # Filter out extension command overrides if the extension isn't installed.
-        filtered = [
-            cmd
-            for cmd in command_templates
-            if self._extension_installed_for_command(cmd["name"])
-        ]
-
-        if not filtered:
-            return {}
-
+        # A preset command template always ships its own body, so it is
+        # self-contained and scaffolds regardless of whether any similarly
+        # named extension is installed. Namespaced names (speckit.<ns>.<cmd>)
+        # are treated exactly like short names (speckit.<cmd>) — they are NOT
+        # filtered out just because ``.specify/extensions/<ns>/`` is absent.
+        # The only command that cannot be materialized is a composition
+        # (prepend/append/wrap) with no base layer to compose onto; that case
+        # is handled per-command below (warn + skip), not by dropping names up
+        # front.
         # Handle composition strategies: resolve composed content for non-replace commands
         resolver = PresetResolver(self.project_root)
         composed_dir = None
         commands_to_register = []
-        for cmd in filtered:
+        for cmd in command_templates:
             strategy = cmd.get("strategy", "replace")
             if strategy != "replace":
                 # Only pre-compose if this preset is the top composing layer.
@@ -907,13 +887,23 @@ def _register_commands(
                             "file": f".composed/{cmd['name']}.md",
                         })
                     else:
-                        raise PresetValidationError(
-                            f"Command '{cmd['name']}' uses '{strategy}' strategy "
-                            f"but no base command layer exists to compose onto. "
-                            f"Ensure a lower-priority preset, extension, or core "
-                            f"command provides this command before using "
-                            f"composition strategies."
+                        # No base layer to compose onto (e.g. the command it
+                        # would wrap comes from an extension that isn't
+                        # installed). Warn and skip this single command rather
+                        # than aborting the whole install — mirrors the
+                        # "composed is None" branch in
+                        # _reconcile_composed_commands so command-mode and
+                        # reconciliation behave identically.
+                        import warnings
+                        warnings.warn(
+                            f"Command '{cmd['name']}' uses '{strategy}' "
+                            f"strategy but no base command layer exists to "
+                            f"compose onto; skipping. Provide a lower-priority "
+                            f"preset, extension, or core command for it before "
+                            f"using composition strategies.",
+                            stacklevel=2,
                         )
+                        continue
                 else:
                     # Not the top layer — register raw file; reconciliation
                     # will overwrite with the correct composed/winning content.
@@ -1681,21 +1671,13 @@ def _reconcile_composed_commands(
         if not command_names:
             return set()
 
-        # Never materialize extension-scoped commands whose extension isn't
-        # installed. Registration (_register_commands / _register_skills)
-        # already refuses them, so a reconciliation pass writing them would
-        # create files no registry entry tracks. Filtering here — the single
-        # chokepoint every install/remove/rescaffold reconciliation funnels
-        # through — keeps all callers consistent without each one re-applying
-        # the filter when seeding names from manifest templates.
-        command_names = [
-            name
-            for name in command_names
-            if self._extension_installed_for_command(name)
-        ]
-        if not command_names:
-            return set()
-
+        # Every preset-owned command name flows through unchanged. Names are
+        # NOT filtered by the ``speckit.<ns>.<cmd>`` shape: a self-contained
+        # preset command scaffolds whether or not a like-named extension is
+        # installed (parity with _register_commands), and a name whose base
+        # layer has disappeared must still reach the loop below so its now
+        # uncomposable stale file gets unregistered. The loop already skips
+        # names that resolve to no layers at all (``if not layers: continue``).
         try:
             from ..agents import CommandRegistrar
         except ImportError:
@@ -2136,14 +2118,11 @@ def _reconcile_skills(
         if not command_names:
             return set()
 
-        command_names = [
-            name
-            for name in command_names
-            if self._extension_installed_for_command(name)
-        ]
-        if not command_names:
-            return set()
-
+        # Preset-owned command names are not filtered by the
+        # ``speckit.<ns>.<cmd>`` shape here either: a self-contained preset
+        # command renders its skill whether or not a like-named extension is
+        # installed. The per-name loop below skips anything that doesn't
+        # resolve to a managed skill directory.
         resolver = PresetResolver(self.project_root)
         active_skills_dir = self._get_skills_dir()
 
@@ -2673,21 +2652,17 @@ def _register_skills(
         if not command_templates:
             return {}
 
-        # Filter out extension command overrides if the extension isn't installed,
-        # matching the same logic used by _register_commands().
-        filtered = [
-            cmd
-            for cmd in command_templates
-            if self._extension_installed_for_command(cmd["name"])
-        ]
-
-        if not filtered:
-            return {}
-
+        # Preset command templates are self-contained and render as skills
+        # regardless of whether a like-named extension is installed — the same
+        # rule _register_commands() uses. No ``speckit.<ns>.<cmd>`` name-shape
+        # filtering; the per-command loop below skips anything without a target
+        # skill directory.
         skills_dir = target_dir if target_dir is not None else self._get_skills_dir()
         if not skills_dir:
             return {}
 
+        resolver = PresetResolver(self.project_root)
+
         from .. import SKILL_DESCRIPTIONS, load_init_options
         from ..agents import CommandRegistrar
         from ..integrations import get_integration
@@ -2717,7 +2692,7 @@ def _register_skills(
 
         written: List[str] = []
 
-        for cmd_tmpl in filtered:
+        for cmd_tmpl in command_templates:
             cmd_name = cmd_tmpl["name"]
             cmd_file_rel = cmd_tmpl["file"]
             source_file = preset_dir / cmd_file_rel
@@ -2757,6 +2732,29 @@ def _register_skills(
             content = source_file.read_text(encoding="utf-8")
             frontmatter, body = registrar.parse_frontmatter(content)
 
+            # A composition-strategy command (wrap/prepend/append) needs a
+            # base layer to compose onto. When _register_commands produced no
+            # composed file for it and the stack still has no base
+            # (resolve_content is None) — e.g. the command it wraps comes from
+            # an extension that isn't installed — rendering the raw preset
+            # fragment as a skill would emit broken output: a literal
+            # {CORE_TEMPLATE} for wrap, or only the preset's own fragment for
+            # prepend/append. Skip it here too so command mode and skills mode
+            # agree (mirrors _register_commands, which skips the same command).
+            # _register_commands already warned for this command in the same
+            # pass, so the skip is silent here to avoid a duplicate warning.
+            effective_strategy = (
+                cmd_tmpl.get("strategy")
+                or frontmatter.get("strategy")
+                or "replace"
+            )
+            if (
+                effective_strategy != "replace"
+                and not composed_file.exists()
+                and resolver.resolve_content(cmd_name, "command") is None
+            ):
+                continue
+
             if frontmatter.get("strategy") == "wrap":
                 body, core_frontmatter = _substitute_core_template(body, cmd_name, self.project_root, registrar)
                 frontmatter = dict(frontmatter)