fix: address review feedback on active-only extension registration

- Restrict the extension-add active-integration fallback to projects
  with no recorded active key at all. A recorded but unsupported key
  (e.g. "generic", deliberately excluded from AGENT_CONFIGS) no longer
  falls back to registering every detected agent.
- Apply the same single-active rule to preset command overrides:
  PresetManager._register_commands now scopes registration to the
  active integration via only_agent.
- Add PresetManager.register_enabled_presets_for_agent, mirroring
  ExtensionManager.register_enabled_extensions_for_agent, and call it
  from integration use/switch/upgrade (active only) alongside the
  existing extension re-registration so presets are rescaffolded on
  activation instead of being written for inactive integrations.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/specify_cli/extensions/__init__.py

@@ -988,9 +988,12 @@ class ExtensionManager:
         init-options gets command files. Non-active integrations receive them
         when selected via ``integration use`` / ``switch`` (rescaffold).
 
-        Projects without a recorded active integration (pre-init-options
+        Projects without a recorded active integration at all (pre-init-options
         layouts or direct library use) fall back to detection-based
-        registration for all agents.
+        registration for all agents. A *recorded* active key that has no
+        registrar config (e.g. ``generic``, which is deliberately excluded
+        from ``AGENT_CONFIGS``) is not treated as "no active integration" —
+        it must not cause registration to target other detected agents.
 
         Returns:
             Mapping of agent name to registered command names, matching the
@@ -1004,7 +1007,7 @@ class ExtensionManager:
             init_options = {}
         active_agent = init_options.get("ai")
 
-        if not active_agent or active_agent not in registrar.AGENT_CONFIGS:
+        if not active_agent:
             return registrar.register_commands_for_all_agents(
                 manifest,
                 extension_dir,
@@ -1013,9 +1016,15 @@ class ExtensionManager:
                 create_missing_active_skills_dir=True,
             )
 
-        agent_config = registrar.AGENT_CONFIGS[active_agent]
+        # A recorded active key with no registrar config (e.g. "generic",
+        # deliberately excluded from AGENT_CONFIGS) has nothing to register
+        # through this path, but it is still an active integration. Passing
+        # it as only_agent below naturally yields no matches instead of
+        # falling back to registering every detected agent.
+        agent_config = registrar.AGENT_CONFIGS.get(active_agent)
         if (
-            is_ai_skills_enabled(init_options)
+            agent_config
+            and is_ai_skills_enabled(init_options)
             and agent_config.get("extension") != "/SKILL.md"
         ):
             # Active agent runs skills mode: extension artifacts render as

src/specify_cli/integrations/_helpers.py

@@ -419,6 +419,38 @@ def _unregister_extensions_for_agent(
     )
 
 
+def _register_presets_for_agent(
+    project_root: Path,
+    agent_key: str,
+    *,
+    continuing: str,
+) -> None:
+    """Register all enabled presets' command overrides/skills for ``agent_key``.
+
+    Presets follow the same single-active rule as extensions (#2948):
+    ``use`` / ``switch`` re-register enabled presets for the agent they
+    activate (rescaffold), so a preset installed while a different
+    integration was active is not left targeting that inactive integration.
+
+    Best-effort: never aborts the surrounding integration operation.
+    """
+    try:
+        from ..presets import PresetManager
+
+        preset_mgr = PresetManager(project_root)
+        preset_mgr.register_enabled_presets_for_agent(agent_key)
+    except Exception as preset_err:
+        from .. import _print_cli_warning
+
+        _print_cli_warning(
+            "register preset artifacts for",
+            "integration",
+            agent_key,
+            preset_err,
+            continuing=continuing,
+        )
+
+
 # ---------------------------------------------------------------------------
 # CLI formatting helpers (re-exported from _commands.py)
 # ---------------------------------------------------------------------------

src/specify_cli/integrations/_migrate_commands.py

@@ -28,6 +28,7 @@ from ._helpers import (
     _read_integration_json,
     _refresh_init_options_speckit_version,
     _register_extensions_for_agent,
+    _register_presets_for_agent,
     _remove_integration_json,
     _resolve_integration_options,
     _resolve_integration_script_type,
@@ -130,6 +131,14 @@ def integration_switch(
                 "need re-registration."
             ),
         )
+        _register_presets_for_agent(
+            project_root,
+            target,
+            continuing=(
+                "The integration switch succeeded, but installed presets may "
+                "need re-registration."
+            ),
+        )
         console.print(f"\n[green]✓[/green] Default integration set to [bold]{target}[/bold].")
         raise typer.Exit(0)
 
@@ -327,6 +336,11 @@ def integration_switch(
         target,
         continuing="The integration switch succeeded, but installed extensions may need re-registration.",
     )
+    _register_presets_for_agent(
+        project_root,
+        target,
+        continuing="The integration switch succeeded, but installed presets may need re-registration.",
+    )
 
     name = (target_integration.config or {}).get("name", target)
     console.print(f"\n[green]✓[/green] Switched to integration '{name}'")
@@ -491,10 +505,10 @@ def integration_upgrade(
         if stale_removed:
             console.print(f"  Removed {len(stale_removed)} stale file(s) from previous install")
 
-    # Re-register enabled extensions only when upgrading the *active*
-    # integration, so its extension commands are (re)created after the
-    # upgrade settled (Phase 2 included). Done outside the try/except above
-    # so this best-effort step cannot affect upgrade success. Non-active
+    # Re-register enabled extensions and presets only when upgrading the
+    # *active* integration, so its command artifacts are (re)created after
+    # the upgrade settled (Phase 2 included). Done outside the try/except
+    # above so this best-effort step cannot affect upgrade success. Non-active
     # integrations are rescaffolded by `use` / `switch` instead — the #2886
     # back-fill for non-active agents was removed at maintainer request
     # (#2948).
@@ -504,6 +518,11 @@ def integration_upgrade(
             key,
             continuing="The integration was upgraded, but installed extensions may need re-registration.",
         )
+        _register_presets_for_agent(
+            project_root,
+            key,
+            continuing="The integration was upgraded, but installed presets may need re-registration.",
+        )
 
     name = (integration.config or {}).get("name", key)
     console.print(f"\n[green]✓[/green] Integration '{name}' upgraded successfully")

src/specify_cli/integrations/_query_commands.py

@@ -18,6 +18,7 @@ from ._commands import integration_app, integration_catalog_app
 from ._helpers import (
     _read_integration_json,
     _register_extensions_for_agent,
+    _register_presets_for_agent,
     _resolve_integration_options,
     _set_default_integration_or_exit,
 )
@@ -248,6 +249,11 @@ def integration_use(
         key,
         continuing="The integration was selected, but installed extensions may need re-registration.",
     )
+    _register_presets_for_agent(
+        project_root,
+        key,
+        continuing="The integration was selected, but installed presets may need re-registration.",
+    )
     console.print(f"[green]✓[/green] Default integration set to [bold]{key}[/bold].")
 
 

src/specify_cli/presets/__init__.py

@@ -28,7 +28,7 @@ from packaging import version as pkg_version
 from packaging.specifiers import SpecifierSet, InvalidSpecifier
 
 from ..extensions import REINSTALL_COMMAND, ExtensionRegistry, normalize_priority
-from .._init_options import is_ai_skills_enabled
+from .._init_options import is_ai_skills_enabled, load_init_options
 from ..integrations.base import IntegrationBase
 from .._utils import dump_frontmatter, version_satisfies
 from ..shared_infra import verify_archive_sha256
@@ -680,10 +680,84 @@ class PresetManager:
             return {}
 
         registrar = CommandRegistrar()
+
+        # Single-active rule (#2948): preset command overrides register for
+        # the active integration only. A project without a recorded active
+        # integration falls back to detection-based registration for all
+        # agents; a recorded key with no registrar config (e.g. "generic")
+        # naturally yields no matches via only_agent instead of falling back.
+        active_agent = load_init_options(self.project_root).get("ai")
         return registrar.register_commands_for_all_agents(
-            commands_to_register, manifest.id, preset_dir, self.project_root
+            commands_to_register,
+            manifest.id,
+            preset_dir,
+            self.project_root,
+            only_agent=active_agent,
         )
 
+    def register_enabled_presets_for_agent(self, agent_name: str) -> None:
+        """Re-register enabled presets' command overrides and skills for ``agent_name``.
+
+        Mirrors ``ExtensionManager.register_enabled_extensions_for_agent`` for
+        presets (#2948): ``integration use`` / ``switch`` call this for the
+        newly active agent so a preset installed while a different
+        integration was active gets rescaffolded on activation, instead of
+        writing artifacts for inactive integrations at install time.
+        ``_register_commands`` / ``_register_skills`` already resolve the
+        active integration from init-options themselves, so this re-runs them
+        for every enabled preset and merges the fresh result for
+        ``agent_name`` into its stored registry metadata.
+        """
+        if not agent_name:
+            return
+
+        resolver = PresetResolver(self.project_root)
+        for pack_id, metadata in self.registry.list_by_priority():
+            pack_dir = self.presets_dir / pack_id
+            manifest = resolver._get_manifest(pack_dir)
+            if manifest is None:
+                continue
+
+            # Isolate per-preset failures: one preset that fails to register
+            # must not abort registration of the remaining enabled presets.
+            try:
+                updates: Dict[str, Any] = {}
+
+                registered_commands = self._register_commands(manifest, pack_dir)
+                existing_commands = metadata.get("registered_commands", {})
+                if not isinstance(existing_commands, dict):
+                    existing_commands = {}
+                merged_commands = copy.deepcopy(existing_commands)
+                if registered_commands.get(agent_name):
+                    merged_commands[agent_name] = registered_commands[agent_name]
+                if merged_commands != existing_commands:
+                    updates["registered_commands"] = merged_commands
+
+                registered_skills = self._register_skills(manifest, pack_dir)
+                if registered_skills:
+                    existing_skills = metadata.get("registered_skills", [])
+                    if not isinstance(existing_skills, list):
+                        existing_skills = []
+                    merged_skills = list(
+                        dict.fromkeys(existing_skills + registered_skills)
+                    )
+                    if merged_skills != existing_skills:
+                        updates["registered_skills"] = merged_skills
+
+                if updates:
+                    self.registry.update(pack_id, updates)
+            except Exception as pack_err:
+                from .. import _print_cli_warning
+
+                _print_cli_warning(
+                    "register preset artifacts for",
+                    "preset",
+                    pack_id,
+                    pack_err,
+                    continuing="Continuing with the remaining presets.",
+                )
+                continue
+
     def _unregister_commands(self, registered_commands: Dict[str, List[str]]) -> None:
         """Remove previously registered command files from agent directories.