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/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].")