Address review: fix init ordering, test coverage, and hermes inventory

- Move agent-context extension install after init-options.json is saved
  so skill registration can read ai_skills + integration key
- Write extension config after install (avoids template overwriting context_file)
- Fix test_defaults_when_markers_field_missing to truly test missing markers key
- Update hermes tests to allow extension-installed agent-context skill

Author: mnriem

src/specify_cli/commands/init.py

@@ -394,8 +394,8 @@ def init(
             ("chmod", "Ensure scripts executable"),
             ("constitution", "Constitution setup"),
             ("git", "Install git extension"),
-            ("agent-context", "Install agent-context extension"),
             ("workflow", "Install bundled workflow"),
+            ("agent-context", "Install agent-context extension"),
             ("final", "Finalize"),
         ]:
             tracker.add(key, label)
@@ -507,28 +507,6 @@ def init(
                 else:
                     tracker.skip("git", "--no-git flag")
 
-                # --- agent-context extension (bundled, auto-installed) ---
-                try:
-                    from ..extensions import ExtensionManager as _ExtMgr
-                    bundled_ac = _locate_bundled_extension("agent-context")
-                    if bundled_ac:
-                        ac_mgr = _ExtMgr(project_path)
-                        if ac_mgr.registry.is_installed("agent-context"):
-                            tracker.complete("agent-context", "already installed")
-                        else:
-                            ac_mgr.install_from_directory(
-                                bundled_ac, get_speckit_version()
-                            )
-                            tracker.complete("agent-context", "extension installed")
-                    else:
-                        tracker.skip("agent-context", "bundled extension not found")
-                except Exception as ac_err:
-                    sanitized_ac = str(ac_err).replace('\n', ' ').strip()
-                    tracker.error(
-                        "agent-context",
-                        f"extension install failed: {sanitized_ac[:120]}",
-                    )
-
                 try:
                     bundled_wf = _locate_bundled_workflow("speckit")
                     if bundled_wf:
@@ -574,8 +552,33 @@ def init(
                     init_opts["ai_skills"] = True
                 save_init_options(project_path, init_opts)
 
+                # --- agent-context extension (bundled, auto-installed) ---
+                # Installed after init-options.json is written so that skill
+                # registration can read ai_skills + integration key.
+                try:
+                    from ..extensions import ExtensionManager as _ExtMgr
+                    bundled_ac = _locate_bundled_extension("agent-context")
+                    if bundled_ac:
+                        ac_mgr = _ExtMgr(project_path)
+                        if ac_mgr.registry.is_installed("agent-context"):
+                            tracker.complete("agent-context", "already installed")
+                        else:
+                            ac_mgr.install_from_directory(
+                                bundled_ac, get_speckit_version()
+                            )
+                            tracker.complete("agent-context", "extension installed")
+                    else:
+                        tracker.skip("agent-context", "bundled extension not found")
+                except Exception as ac_err:
+                    sanitized_ac = str(ac_err).replace('\n', ' ').strip()
+                    tracker.error(
+                        "agent-context",
+                        f"extension install failed: {sanitized_ac[:120]}",
+                    )
+
                 # Write context_file to the agent-context extension config
-                # (not init-options.json — that is the legacy location).
+                # AFTER the extension install (which copies the template config
+                # with an empty context_file).
                 if resolved_integration.context_file:
                     _update_agent_context_config_file(
                         project_path,

tests/extensions/test_extension_agent_context.py

@@ -115,7 +115,13 @@ def test_defaults_when_ext_config_missing(self, tmp_path):
         assert end == IntegrationBase.CONTEXT_MARKER_END
 
     def test_defaults_when_markers_field_missing(self, tmp_path):
-        _write_ext_config(tmp_path, context_file="CLAUDE.md")
+        """Config file exists with context_file but no context_markers key."""
+        cfg_path = (
+            tmp_path / ".specify" / "extensions" / "agent-context"
+            / "agent-context-config.yml"
+        )
+        cfg_path.parent.mkdir(parents=True, exist_ok=True)
+        cfg_path.write_text("context_file: CLAUDE.md\n", encoding="utf-8")
         i = _CtxIntegration()
         start, end = i._resolve_context_markers(tmp_path)
         assert start == IntegrationBase.CONTEXT_MARKER_START

tests/integrations/test_integration_copilot.py

@@ -644,9 +644,9 @@ def test_complete_file_inventory_skills_sh(self, tmp_path):
         assert result.exit_code == 0, f"init failed: {result.output}"
         actual = sorted(p.relative_to(project).as_posix() for p in project.rglob("*") if p.is_file())
         expected = sorted([
-            # Skill files (core commands only — extension commands are not
-            # rendered as skills, they live in .specify/extensions/)
+            # Skill files (core + extension-installed agent-context command)
             *[f".github/skills/speckit-{cmd}/SKILL.md" for cmd in self._SKILL_COMMANDS],
+            ".github/skills/speckit-agent-context-update/SKILL.md",
             # Context file
             ".github/copilot-instructions.md",
             # Bundled agent-context extension

tests/integrations/test_integration_hermes.py

@@ -241,10 +241,15 @@ def test_complete_file_inventory_sh(self, tmp_path, monkeypatch):
             p.relative_to(project).as_posix()
             for p in project.rglob("*") if p.is_file()
         )
-        # Ensure no .hermes/skills/speckit-*/SKILL.md in project dir
-        hermes_skill_files = [f for f in actual if f.startswith(".hermes/skills/speckit-")]
+        # Ensure no core .hermes/skills/speckit-*/SKILL.md in project dir
+        # (extension-installed skills like agent-context-update may appear)
+        hermes_skill_files = [
+            f for f in actual
+            if f.startswith(".hermes/skills/speckit-")
+            and "agent-context" not in f
+        ]
         assert hermes_skill_files == [], (
-            f"Expected no local SKILL.md files, found: {hermes_skill_files}"
+            f"Expected no local core SKILL.md files, found: {hermes_skill_files}"
         )
         # Ensure the marker exists (empty dir won't appear in file listing)
         assert (project / ".hermes" / "skills").is_dir()
@@ -274,9 +279,15 @@ def test_complete_file_inventory_ps(self, tmp_path, monkeypatch):
             p.relative_to(project).as_posix()
             for p in project.rglob("*") if p.is_file()
         )
-        hermes_skill_files = [f for f in actual if f.startswith(".hermes/skills/speckit-")]
+        # Ensure no core .hermes/skills/speckit-*/SKILL.md in project dir
+        # (extension-installed skills like agent-context-update may appear)
+        hermes_skill_files = [
+            f for f in actual
+            if f.startswith(".hermes/skills/speckit-")
+            and "agent-context" not in f
+        ]
         assert hermes_skill_files == [], (
-            f"Expected no local SKILL.md files, found: {hermes_skill_files}"
+            f"Expected no local core SKILL.md files, found: {hermes_skill_files}"
         )
         assert (project / ".hermes" / "skills").is_dir()
 
@@ -342,6 +353,10 @@ def test_ai_hermes_without_ai_skills_auto_promotes(self, tmp_path, monkeypatch):
         assert (home / ".hermes" / "skills" / "speckit-plan" / "SKILL.md").exists()
         # Local marker should exist
         assert (target / ".hermes" / "skills").is_dir()
-        # No SKILL.md files in project-local dir
-        local_skills = list((target / ".hermes" / "skills").iterdir())
+        # No core SKILL.md files in project-local dir
+        # (extension-installed skills like agent-context-update may appear)
+        local_skills = [
+            d for d in (target / ".hermes" / "skills").iterdir()
+            if "agent-context" not in d.name
+        ]
         assert local_skills == [], f"Local skills dir should be empty, got: {local_skills}"