feat: setup() owns scaffolding and returns actual installed files

- AgentBootstrap._scaffold_project() calls scaffold_from_core_pack,
  snapshots before/after, returns all new files
- finalize_setup() filters agent_files to only track files under the
  agent's own directory tree (shared .specify/ files not tracked)
- All 25 bootstrap setup() methods call _scaffold_project() and return
  the actual file list instead of []
- --agent init flow routes through setup() for scaffolding instead of
  calling scaffold_from_core_pack directly
- 100 new tests (TestSetupReturnsFiles): verify every agent's setup()
  returns non-empty, existing, absolute paths including agent-dir files
- Parity tests use CliRunner to invoke the real init command
- finalize_setup bug fix: skills-migrated agents (agy) now have their
  skills directory scanned correctly
- 1262 tests pass (452 in test_agent_pack.py alone)

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
Agent-Logs-Url: https://github.com/github/spec-kit/sessions/054690bb-c048-41e0-b553-377d5cb36b78

src/specify_cli/__init__.py

@@ -1984,7 +1984,10 @@ def init(
             "This will become the default in v0.6.0."
         )
 
-    if use_github:
+    if use_agent_pack:
+        # Pack-based flow: setup() owns scaffolding, always uses bundled assets.
+        tracker.add("scaffold", "Apply bundled assets")
+    elif use_github:
         for key, label in [
             ("fetch", "Fetch latest release"),
             ("download", "Download template"),
@@ -2019,7 +2022,26 @@ def init(
             verify = not skip_tls
             local_ssl_context = ssl_context if verify else False
 
-            if use_github:
+            # -- scaffolding ------------------------------------------------
+            # Pack-based flow (--agent): setup() owns scaffolding and
+            # returns every file it created.  Legacy flow (--ai): scaffold
+            # directly or download from GitHub.
+            agent_setup_files: list[Path] = []
+
+            if use_agent_pack and agent_bootstrap is not None:
+                tracker.start("scaffold")
+                try:
+                    agent_setup_files = agent_bootstrap.setup(
+                        project_path, selected_script, {"here": here})
+                    tracker.complete(
+                        "scaffold",
+                        f"{selected_ai} ({len(agent_setup_files)} files)")
+                except Exception as exc:
+                    tracker.error("scaffold", str(exc))
+                    if not here and project_path.exists():
+                        shutil.rmtree(project_path)
+                    raise typer.Exit(1)
+            elif use_github:
                 with httpx.Client(verify=local_ssl_context) as local_client:
                     download_and_extract_template(project_path, selected_ai, selected_script, here, verbose=False, tracker=tracker, client=local_client, debug=debug, github_token=github_token)
             else:
@@ -2162,11 +2184,14 @@ def init(
                 tracker.skip("cleanup", "not needed (no download)")
 
             # When --agent is used, record all installed agent files for
-            # tracked teardown.  This runs AFTER the full init pipeline has
-            # finished creating files (scaffolding, skills, presets,
-            # extensions) so finalize_setup captures everything.
+            # tracked teardown.  setup() already returned the files it
+            # created; pass them to finalize_setup so the manifest is
+            # accurate.  finalize_setup also scans the agent directory
+            # to catch any additional files created by later pipeline
+            # steps (skills, extensions, presets).
             if use_agent_pack and agent_bootstrap is not None:
-                agent_bootstrap.finalize_setup(project_path)
+                agent_bootstrap.finalize_setup(
+                    project_path, agent_files=agent_setup_files)
 
             tracker.complete("final", "project ready")
         except (typer.Exit, SystemExit):