feat: update Bob integration to skills-based layout for Bob 2.0

integrations/catalog.json

@@ -177,11 +177,11 @@
     "bob": {
       "id": "bob",
       "name": "IBM Bob",
-      "version": "1.0.0",
-      "description": "IBM Bob IDE integration",
+      "version": "2.0.0",
+      "description": "IBM Bob 2.0 IDE skills-based integration",
       "author": "spec-kit-core",
       "repository": "https://github.com/github/spec-kit",
-      "tags": ["ide", "ibm"]
+      "tags": ["ide", "ibm", "skills"]
     },
     "trae": {
       "id": "trae",

src/specify_cli/_invocation_style.py

@@ -18,6 +18,7 @@
 CONDITIONAL_SLASH_AGENTS: frozenset[str] = frozenset(
     {
         "agy",
+        "bob",
         "claude",
         "copilot",
         "cursor-agent",

src/specify_cli/agents.py

@@ -637,6 +637,49 @@ def register_commands(
         is_cline_ext = agent_name == "cline" and source_id != "core"
         source_root = source_dir.resolve()
 
+        # Resolve the command-reference separator once for this agent/project.
+        # Dual-layout agents (e.g. Bob) use different separators for their
+        # skills vs command layouts, so we ask the integration to map the
+        # project's persisted skills state to the correct separator rather than
+        # relying on the single static AGENT_CONFIGS value.
+        _sep = agent_config.get("invoke_separator", ".")
+        try:
+            from specify_cli.integrations import get_integration  # noqa: PLC0415
+
+            _integ = get_integration(agent_name)
+            if _integ is not None:
+                _opts = load_init_options(project_root)
+                # The persisted ``ai_skills`` flag describes only the active
+                # integration (``opts["ai"]``).  ``register_commands_for_all_agents``
+                # calls this for every detected agent, so trusting that flag for a
+                # different agent would, e.g., render a legacy ``.bob/commands``
+                # project's refs as ``/speckit-*`` just because Copilot is active in
+                # skills mode.  Only consult the flag for the agent it describes;
+                # otherwise resolve this agent's separator from its own project-aware
+                # detection.
+                if _opts.get("ai") == agent_name:
+                    _sep = _integ.invoke_separator_for_mode(
+                        is_ai_skills_enabled(_opts)
+                    )
+                else:
+                    # Inactive agent: the reference separator must match the
+                    # layout THIS registrar writes into — determined by the
+                    # agent's static output config (its command dir + file
+                    # extension), not by unrelated sibling directories on disk.
+                    # A skill-scaffold output ("/SKILL.md") uses the skills
+                    # separator; a command-layout output uses the command
+                    # separator. This avoids mislabeling a Bob command-layout
+                    # write as skills just because an unrelated .bob/skills
+                    # directory happens to exist.
+                    registrar_writes_skills = (
+                        agent_config.get("extension") == "/SKILL.md"
+                    )
+                    _sep = _integ.invoke_separator_for_mode(
+                        registrar_writes_skills
+                    )
+        except Exception:
+            pass
+
         for cmd_info in commands:
             cmd_name = cmd_info["name"]
             aliases = cmd_info.get("aliases", [])
@@ -709,13 +752,15 @@ def register_commands(
             )
 
             # Resolve __SPECKIT_COMMAND_*__ tokens using the agent's invoke separator.
-            # The separator is sourced from agent_config (populated by _build_agent_configs,
-            # which propagates each integration's invoke_separator class attribute).
+            # For dual-layout agents (e.g. Bob) the separator differs between the
+            # skills and command layouts, so a single static AGENT_CONFIGS value is
+            # insufficient. Resolve it from the integration using the project's
+            # persisted skills state; single-layout agents fall back to the static
+            # AGENT_CONFIGS value unchanged (invoke_separator_for_mode default).
             # Deferred import of IntegrationBase avoids a circular import at module load
             # (base.py itself imports CommandRegistrar lazily).
             from specify_cli.integrations.base import IntegrationBase  # noqa: PLC0415
 
-            _sep = agent_config.get("invoke_separator", ".")
             body = IntegrationBase.resolve_command_refs(body, _sep)
 
             output_name = self._compute_output_name(agent_name, cmd_name, agent_config)

src/specify_cli/commands/init.py

@@ -458,6 +458,7 @@ def init(
                     script_type=selected_script,
                     raw_options=integration_options,
                     parsed_options=integration_parsed_options or None,
+                    project_root=project_path,
                 )
                 _write_integration_json(
                     project_path,
@@ -478,7 +479,7 @@ def init(
                     tracker=tracker,
                     force=force,
                     invoke_separator=resolved_integration.effective_invoke_separator(
-                        integration_parsed_options
+                        integration_parsed_options, project_root=project_path
                     ),
                 )
                 tracker.complete(
@@ -532,10 +533,8 @@ def init(
                     "feature_numbering": "sequential",
                     "speckit_version": get_speckit_version(),
                 }
-                from ..integrations.base import SkillsIntegration as _SkillsPersist
-
-                if isinstance(resolved_integration, _SkillsPersist) or getattr(
-                    resolved_integration, "_skills_mode", False
+                if resolved_integration.is_skills_mode(
+                    integration_parsed_options or None, project_root=project_path
                 ):
                     init_opts["ai_skills"] = True
                 save_init_options(project_path, init_opts)
@@ -683,11 +682,9 @@ def init(
             steps_lines.append("1. You're already in the project directory!")
             step_num = 2
 
-        from ..integrations.base import SkillsIntegration as _SkillsInt
-
-        _is_skills_integration = isinstance(
-            resolved_integration, _SkillsInt
-        ) or getattr(resolved_integration, "_skills_mode", False)
+        _is_skills_integration = resolved_integration.is_skills_mode(
+            integration_parsed_options or None, project_root=project_path
+        )
 
         codex_skill_mode = selected_ai == "codex" and _is_skills_integration
         zcode_skill_mode = selected_ai == "zcode" and _is_skills_integration
@@ -703,6 +700,7 @@ def init(
         zed_skill_mode = selected_ai == "zed" and _is_skills_integration
         grok_skill_mode = selected_ai == "grok" and _is_skills_integration
         cline_skill_mode = selected_ai == "cline"
+        bob_skill_mode = selected_ai == "bob" and _is_skills_integration
         native_skill_mode = (
             codex_skill_mode
             or zcode_skill_mode
@@ -715,6 +713,7 @@ def init(
             or devin_skill_mode
             or zed_skill_mode
             or grok_skill_mode
+            or bob_skill_mode
         )
 
         if codex_skill_mode:
@@ -752,6 +751,11 @@ def init(
                 f"{step_num}. Start Grok Build in this project directory; spec-kit skills were installed to [cyan].grok/skills[/cyan]"
             )
             step_num += 1
+        if bob_skill_mode:
+            steps_lines.append(
+                f"{step_num}. Start Bob in this project directory; spec-kit skills were installed to [cyan].bob/skills[/cyan]"
+            )
+            step_num += 1
         usage_label = "skills" if native_skill_mode else "slash commands"
 
         from .._invocation_style import (

src/specify_cli/integration_runtime.py

@@ -46,6 +46,7 @@ def with_integration_setting(
     script_type: str | None = None,
     raw_options: str | None = None,
     parsed_options: dict[str, Any] | None = None,
+    project_root: Any = None,
 ) -> dict[str, dict[str, Any]]:
     """Return integration settings with *key* updated."""
     settings = integration_settings(state)
@@ -63,7 +64,9 @@ def with_integration_setting(
     elif raw_options is not None:
         current.pop("parsed_options", None)
 
-    current["invoke_separator"] = integration.effective_invoke_separator(parsed_options)
+    current["invoke_separator"] = integration.effective_invoke_separator(
+        parsed_options, project_root
+    )
     settings[key] = current
     return settings
 
@@ -73,10 +76,11 @@ def invoke_separator_for_integration(
     state: dict[str, Any],
     key: str,
     parsed_options: dict[str, Any] | None = None,
+    project_root: Any = None,
 ) -> str:
     """Resolve the invocation separator for stored/default integration state."""
     if parsed_options is not None:
-        return integration.effective_invoke_separator(parsed_options)
+        return integration.effective_invoke_separator(parsed_options, project_root)
 
     setting = integration_setting(state, key)
     stored_separator = setting.get("invoke_separator")
@@ -85,6 +89,6 @@ def invoke_separator_for_integration(
 
     stored_parsed = setting.get("parsed_options")
     if isinstance(stored_parsed, dict):
-        return integration.effective_invoke_separator(stored_parsed)
+        return integration.effective_invoke_separator(stored_parsed, project_root)
 
-    return integration.effective_invoke_separator(None)
+    return integration.effective_invoke_separator(None, project_root)

src/specify_cli/integrations/_helpers.py

@@ -272,24 +272,19 @@ def _update_init_options_for_integration(
         load_init_options,
         save_init_options,
     )
-    from .base import SkillsIntegration
     opts = load_init_options(project_root)
     opts["integration"] = integration.key
     opts["ai"] = integration.key
     opts["speckit_version"] = _get_speckit_version()
     if script_type:
         opts["script"] = script_type
-    # Skills mode is either intrinsic (SkillsIntegration), set on the instance
-    # during setup() (_skills_mode), or requested via parsed options (e.g.
-    # Copilot's --skills, persisted as parsed_options["skills"]). The latter is
-    # the only signal available on the `use` path, where no setup() runs and a
-    # fresh integration instance has _skills_mode == False (issue #3550).
-    skills_mode = (
-        isinstance(integration, SkillsIntegration)
-        or getattr(integration, "_skills_mode", False)
-        or bool((parsed_options or {}).get("skills"))
-    )
-    if skills_mode:
+    # Whether skills mode is active is owned by each integration via the
+    # ``is_skills_mode`` hook (base default honors ``--skills``;
+    # SkillsIntegration returns True; skills-first integrations with a legacy
+    # opt-out such as Bob override it). This keeps shared code free of
+    # ``isinstance`` / ``_skills_mode`` probing. Passing parsed_options lets it
+    # work on the ``use``/``install`` path where no setup() runs (issue #3550).
+    if integration.is_skills_mode(parsed_options, project_root=project_root):
         opts["ai_skills"] = True
     else:
         opts.pop("ai_skills", None)
@@ -325,6 +320,7 @@ def _set_default_integration(
         script_type=resolved_script,
         raw_options=raw_options,
         parsed_options=parsed_options,
+        project_root=project_root,
     )
 
     if refresh_templates:
@@ -333,7 +329,8 @@ def _set_default_integration(
                 project_root,
                 resolved_script,
                 invoke_separator=_invoke_separator_for_integration(
-                    integration, {"integration_settings": settings}, key, parsed_options
+                    integration, {"integration_settings": settings}, key, parsed_options,
+                    project_root=project_root,
                 ),
                 force=refresh_templates_force,
                 refresh_managed=True,

src/specify_cli/integrations/_install_commands.py

@@ -127,7 +127,8 @@ def integration_install(
         project_root,
         selected_script,
         invoke_separator=_invoke_separator_for_integration(
-            infra_integration, current, infra_key, infra_parsed
+            infra_integration, current, infra_key, infra_parsed,
+            project_root=project_root,
         ),
     )
     if os.name != "nt":
@@ -155,10 +156,16 @@ def integration_install(
             script_type=selected_script,
             raw_options=raw_options,
             parsed_options=parsed_options,
+            project_root=project_root,
         )
         _write_integration_json(project_root, new_default, new_installed, settings)
         if new_default == integration.key:
-            _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+            _update_init_options_for_integration(
+                project_root,
+                integration,
+                script_type=selected_script,
+                parsed_options=parsed_options,
+            )
         else:
             _refresh_init_options_speckit_version(project_root)
 

src/specify_cli/integrations/_migrate_commands.py

@@ -236,7 +236,8 @@ def integration_switch(
         force=refresh_shared_infra,
         refresh_managed=True,
         invoke_separator=_invoke_separator_for_integration(
-            target_integration, current, target, parsed_options
+            target_integration, current, target, parsed_options,
+            project_root=project_root,
         ),
         refresh_hint=(
             "To overwrite customizations, re-run with "
@@ -415,7 +416,8 @@ def integration_upgrade(
         selected_script,
         force=force,
         invoke_separator=_invoke_separator_for_integration(
-            infra_integration, current, infra_key, infra_parsed
+            infra_integration, current, infra_key, infra_parsed,
+            project_root=project_root,
         ),
     )
     if os.name != "nt":
@@ -441,14 +443,16 @@ def integration_upgrade(
             script_type=selected_script,
             raw_options=raw_options,
             parsed_options=parsed_options,
+            project_root=project_root,
         )
         if installed_key == key:
             try:
                 _install_shared_infra(
                     project_root,
                     selected_script,
                     invoke_separator=_invoke_separator_for_integration(
-                        integration, {"integration_settings": settings}, key, parsed_options
+                        integration, {"integration_settings": settings}, key, parsed_options,
+                        project_root=project_root,
                     ),
                     force=force,
                     refresh_managed=True,
@@ -463,7 +467,12 @@ def integration_upgrade(
         new_manifest.save()
         _write_integration_json(project_root, installed_key, installed_keys, settings)
         if installed_key == key:
-            _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+            _update_init_options_for_integration(
+                project_root,
+                integration,
+                script_type=selected_script,
+                parsed_options=parsed_options,
+            )
         else:
             _refresh_init_options_speckit_version(project_root)
     except Exception as exc: