feat: add --agent flag to init for pack-based flow with file tracking

- `specify init --agent claude` resolves through the pack system and
  records all installed files in .specify/agent-manifest-<id>.json via
  finalize_setup() after the init pipeline finishes
- --agent and --ai are mutually exclusive; --agent additionally enables
  tracked teardown/switch
- init-options.json gains "agent_pack" key when --agent is used
- 4 new parity tests verify: pack resolution matches AGENT_CONFIG,
  commands_dir parity, finalize_setup records pipeline-created files,
  pack metadata matches CommandRegistrar configuration

Co-authored-by: mnriem <15701806+mnriem@users.noreply.github.com>
Agent-Logs-Url: https://github.com/github/spec-kit/sessions/930d8c4d-ce42-41fb-a40f-561fb1468e81

Author: Copilot

src/specify_cli/__init__.py

@@ -1715,6 +1715,7 @@ def _handle_agent_skills_migration(console: Console, agent_key: str) -> None:
 def init(
     project_name: str = typer.Argument(None, help="Name for your new project directory (optional if using --here, or use '.' for current directory)"),
     ai_assistant: str = typer.Option(None, "--ai", help=AI_ASSISTANT_HELP),
+    agent: str = typer.Option(None, "--agent", help="AI agent to use (pack-based flow — resolves through the agent pack system and records installed files for tracked teardown). Accepts the same agent IDs as --ai."),
     ai_commands_dir: str = typer.Option(None, "--ai-commands-dir", help="Directory for agent command files (required with --ai generic, e.g. .myagent/commands/)"),
     script_type: str = typer.Option(None, "--script", help="Script type to use: sh or ps"),
     ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for AI agent tools like Claude Code"),
@@ -1753,6 +1754,7 @@ def init(
     Examples:
         specify init my-project
         specify init my-project --ai claude
+        specify init my-project --agent claude  # Pack-based flow (with file tracking)
         specify init my-project --ai copilot --no-git
         specify init --ignore-agent-tools my-project
         specify init . --ai claude         # Initialize in current directory
@@ -1765,13 +1767,25 @@ def init(
         specify init --here --force  # Skip confirmation when current directory not empty
         specify init my-project --ai claude --ai-skills   # Install agent skills
         specify init --here --ai gemini --ai-skills
+        specify init my-project --agent claude --ai-skills  # Pack-based flow with skills
         specify init my-project --ai generic --ai-commands-dir .myagent/commands/  # Unsupported agent
         specify init my-project --offline  # Use bundled assets (no network access)
         specify init my-project --ai claude --preset healthcare-compliance  # With preset
     """
 
     show_banner()
 
+    # --agent and --ai are interchangeable for agent selection, but --agent
+    # additionally opts into the pack-based flow (file tracking via
+    # finalize_setup for tracked teardown/switch).
+    use_agent_pack = False
+    if agent:
+        if ai_assistant:
+            console.print("[red]Error:[/red] --agent and --ai cannot both be specified. Use one or the other.")
+            raise typer.Exit(1)
+        ai_assistant = agent
+        use_agent_pack = True
+
     # Detect when option values are likely misinterpreted flags (parameter ordering issue)
     if ai_assistant and ai_assistant.startswith("--"):
         console.print(f"[red]Error:[/red] Invalid value for --ai: '{ai_assistant}'")
@@ -1802,7 +1816,7 @@ def init(
         raise typer.Exit(1)
 
     if ai_skills and not ai_assistant:
-        console.print("[red]Error:[/red] --ai-skills requires --ai to be specified")
+        console.print("[red]Error:[/red] --ai-skills requires --ai or --agent to be specified")
         console.print("[yellow]Usage:[/yellow] specify init <project> --ai <agent> --ai-skills")
         raise typer.Exit(1)
 
@@ -1854,6 +1868,19 @@ def init(
             "copilot"
         )
 
+    # When --agent is used, validate that the agent resolves through the pack
+    # system and prepare the bootstrap for post-init file tracking.
+    agent_bootstrap = None
+    if use_agent_pack:
+        from .agent_pack import resolve_agent_pack, load_bootstrap, PackResolutionError, AgentPackError
+        try:
+            resolved = resolve_agent_pack(selected_ai)
+            agent_bootstrap = load_bootstrap(resolved.path, resolved.manifest)
+            console.print(f"[dim]Pack-based flow: {resolved.manifest.name} ({resolved.source})[/dim]")
+        except (PackResolutionError, AgentPackError) as exc:
+            console.print(f"[red]Error resolving agent pack:[/red] {exc}")
+            raise typer.Exit(1)
+
     # Agents that have moved from explicit commands/prompts to agent skills.
     if selected_ai in AGENT_SKILLS_MIGRATIONS and not ai_skills:
         # If selected interactively (no --ai provided), automatically enable
@@ -2090,6 +2117,7 @@ def init(
                 "ai": selected_ai,
                 "ai_skills": ai_skills,
                 "ai_commands_dir": ai_commands_dir,
+                "agent_pack": use_agent_pack,
                 "branch_numbering": branch_numbering or "sequential",
                 "here": here,
                 "preset": preset,
@@ -2133,6 +2161,13 @@ def init(
             if not use_github:
                 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.
+            if use_agent_pack and agent_bootstrap is not None:
+                agent_bootstrap.finalize_setup(project_path)
+
             tracker.complete("final", "project ready")
         except (typer.Exit, SystemExit):
             raise

tests/test_agent_pack.py

@@ -808,3 +808,109 @@ def test_check_detects_extension_file_modification(self, tmp_path):
         modified = check_modified_files(project, "ag")
         assert len(modified) == 1
         assert ".ag/ext.md" in modified[0]
+
+
+# ===================================================================
+# --agent flag on init (pack-based flow parity)
+# ===================================================================
+
+class TestInitAgentFlag:
+    """Verify the --agent flag on ``specify init`` resolves through the
+    pack system and that pack metadata is consistent with AGENT_CONFIG."""
+
+    def test_agent_resolves_same_agent_as_ai(self):
+        """--agent <id> resolves the same agent as --ai <id> for all
+        agents in AGENT_CONFIG (except 'generic')."""
+        from specify_cli import AGENT_CONFIG
+
+        for agent_id in AGENT_CONFIG:
+            if agent_id == "generic":
+                continue
+            try:
+                resolved = resolve_agent_pack(agent_id)
+            except PackResolutionError:
+                pytest.fail(f"--agent {agent_id} would fail: no pack found")
+
+            assert resolved.manifest.id == agent_id
+
+    def test_pack_commands_dir_matches_agent_config(self):
+        """The pack's commands_dir matches the directory that the old
+        flow (AGENT_CONFIG) would use, ensuring both flows write files
+        to the same location."""
+        from specify_cli import AGENT_CONFIG
+
+        for agent_id, config in AGENT_CONFIG.items():
+            if agent_id == "generic":
+                continue
+            try:
+                resolved = resolve_agent_pack(agent_id)
+            except PackResolutionError:
+                continue
+
+            # AGENT_CONFIG stores folder + commands_subdir
+            folder = config.get("folder", "").rstrip("/")
+            subdir = config.get("commands_subdir", "commands")
+            expected_dir = f"{folder}/{subdir}" if folder else ""
+            # Normalise path separators
+            expected_dir = expected_dir.lstrip("/")
+
+            assert resolved.manifest.commands_dir == expected_dir, (
+                f"{agent_id}: commands_dir mismatch: "
+                f"pack={resolved.manifest.commands_dir!r} "
+                f"config_derived={expected_dir!r}"
+            )
+
+    def test_finalize_setup_records_files_after_init(self, tmp_path):
+        """Simulates the --agent init flow: setup → create files →
+        finalize_setup, then verifies the install manifest is present."""
+        # Pick any embedded agent (claude)
+        resolved = resolve_agent_pack("claude")
+        bootstrap = load_bootstrap(resolved.path, resolved.manifest)
+
+        project = tmp_path / "project"
+        project.mkdir()
+        (project / ".specify").mkdir()
+
+        # setup() creates the directory structure
+        setup_files = bootstrap.setup(project, "sh", {})
+        assert isinstance(setup_files, list)
+
+        # Simulate the init pipeline creating command files
+        commands_dir = project / resolved.manifest.commands_dir
+        commands_dir.mkdir(parents=True, exist_ok=True)
+        cmd_file = commands_dir / "speckit-plan.md"
+        cmd_file.write_text("plan command", encoding="utf-8")
+
+        # finalize_setup records everything
+        bootstrap.finalize_setup(project)
+
+        manifest_file = _manifest_path(project, "claude")
+        assert manifest_file.is_file()
+
+        data = json.loads(manifest_file.read_text(encoding="utf-8"))
+        all_tracked = {
+            **data.get("agent_files", {}),
+            **data.get("extension_files", {}),
+        }
+        assert any("speckit-plan.md" in p for p in all_tracked), (
+            "finalize_setup should record files created by the init pipeline"
+        )
+
+    def test_pack_metadata_enables_same_extension_registration(self):
+        """Pack command_registration metadata matches CommandRegistrar
+        configuration, ensuring that extension registration via the pack
+        system writes to the same directories and with the same format as
+        the old AGENT_CONFIG-based flow."""
+        from specify_cli.agents import CommandRegistrar
+
+        for manifest in list_embedded_agents():
+            registrar_config = CommandRegistrar.AGENT_CONFIGS.get(manifest.id)
+            if registrar_config is None:
+                continue
+
+            # These four fields are what CommandRegistrar uses to render
+            # extension commands — they must match exactly.
+            assert manifest.commands_dir == registrar_config["dir"]
+            assert manifest.command_format == registrar_config["format"]
+            assert manifest.arg_placeholder == registrar_config["args"]
+            assert manifest.file_extension == registrar_config["extension"]