fix(ai-skills): exclude non-speckit copilot agent markdown from skill… (#1867)

* fix(ai-skills): exclude non-speckit copilot agent markdown from skill generation

* Potential fix for pull request finding

Fix missing `.agent` filename suffix

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* Fix test assertion speckit.plan.md to speckit.plan.agent


Fix test assertion speckit.plan.md to speckit.plan.agent

* Fix filter glob based on review suggestions

fix(ai-skills): normalize Copilot .agent template names and align template fallback filtering

* Add template glob for fallback directory

* GH Copilot Suggestions

Clarify comment regarding Copilot's use of templates in tests.
Add extra test assertion

* fix(ai-skills): normalize Copilot .agent templates and preserve fallback behavior

fix(ai-skills): handle Copilot .agent templates and fallback filtering

Normalize Copilot command template names by stripping the .agent suffix
when deriving skill names and metadata sources, so files like
speckit.plan.agent.md produce speckit-plan and map to plan.md metadata.

Also align Copilot template discovery with speckit.* filtering while
preserving fallback to templates/commands/ when .github/agents contains
only user-authored markdown files, and add regression coverage for both
non-speckit agent exclusion and fallback behavior.

* fix(ai-skills): ignore non-speckit markdown commands

---------

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Author: darkglow-net

src/specify_cli/__init__.py

@@ -1256,23 +1256,29 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
     else:
         templates_dir = project_path / commands_subdir
 
-    if not templates_dir.exists() or not any(templates_dir.glob("*.md")):
+    # Only consider speckit.*.md templates so that user-authored command
+    # files (e.g. custom slash commands, agent files) coexisting in the
+    # same commands directory are not incorrectly converted into skills.
+    template_glob = "speckit.*.md"
+
+    if not templates_dir.exists() or not any(templates_dir.glob(template_glob)):
         # Fallback: try the repo-relative path (for running from source checkout)
         # This also covers agents whose extracted commands are in a different
         # format (e.g. gemini/tabnine use .toml, not .md).
         script_dir = Path(__file__).parent.parent.parent  # up from src/specify_cli/
         fallback_dir = script_dir / "templates" / "commands"
         if fallback_dir.exists() and any(fallback_dir.glob("*.md")):
             templates_dir = fallback_dir
+            template_glob = "*.md"
 
-    if not templates_dir.exists() or not any(templates_dir.glob("*.md")):
+    if not templates_dir.exists() or not any(templates_dir.glob(template_glob)):
         if tracker:
             tracker.error("ai-skills", "command templates not found")
         else:
             console.print("[yellow]Warning: command templates not found, skipping skills installation[/yellow]")
         return False
 
-    command_files = sorted(templates_dir.glob("*.md"))
+    command_files = sorted(templates_dir.glob(template_glob))
     if not command_files:
         if tracker:
             tracker.skip("ai-skills", "no command templates found")
@@ -1311,11 +1317,14 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
                 body = content
 
             command_name = command_file.stem
-            # Normalize: extracted commands may be named "speckit.<cmd>.md";
-            # strip the "speckit." prefix so skill names stay clean and
+            # Normalize: extracted commands may be named "speckit.<cmd>.md"
+            # or "speckit.<cmd>.agent.md"; strip the "speckit." prefix and
+            # any trailing ".agent" suffix so skill names stay clean and
             # SKILL_DESCRIPTIONS lookups work.
             if command_name.startswith("speckit."):
                 command_name = command_name[len("speckit."):]
+            if command_name.endswith(".agent"):
+                command_name = command_name[:-len(".agent")]
             # Kimi CLI discovers skills by directory name and invokes them as
             # /skill:<name> — use dot separator to match packaging convention.
             if selected_ai == "kimi":
@@ -1340,6 +1349,8 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
             source_name = command_file.name
             if source_name.startswith("speckit."):
                 source_name = source_name[len("speckit."):]
+            if source_name.endswith(".agent.md"):
+                source_name = source_name[:-len(".agent.md")] + ".md"
 
             frontmatter_data = {
                 "name": skill_name,

tests/test_ai_skills.py

@@ -62,7 +62,7 @@ def templates_dir(project_dir):
     tpl_root.mkdir(parents=True, exist_ok=True)
 
     # Template with valid YAML frontmatter
-    (tpl_root / "specify.md").write_text(
+    (tpl_root / "speckit.specify.md").write_text(
         "---\n"
         "description: Create or update the feature specification.\n"
         "handoffs:\n"
@@ -79,7 +79,7 @@ def templates_dir(project_dir):
     )
 
     # Template with minimal frontmatter
-    (tpl_root / "plan.md").write_text(
+    (tpl_root / "speckit.plan.md").write_text(
         "---\n"
         "description: Generate implementation plan.\n"
         "---\n"
@@ -91,15 +91,15 @@ def templates_dir(project_dir):
     )
 
     # Template with no frontmatter
-    (tpl_root / "tasks.md").write_text(
+    (tpl_root / "speckit.tasks.md").write_text(
         "# Tasks Command\n"
         "\n"
         "Body without frontmatter.\n",
         encoding="utf-8",
     )
 
     # Template with empty YAML frontmatter (yaml.safe_load returns None)
-    (tpl_root / "empty_fm.md").write_text(
+    (tpl_root / "speckit.empty_fm.md").write_text(
         "---\n"
         "---\n"
         "\n"
@@ -337,7 +337,7 @@ def test_malformed_yaml_frontmatter(self, project_dir):
         cmds_dir = project_dir / ".claude" / "commands"
         cmds_dir.mkdir(parents=True)
 
-        (cmds_dir / "broken.md").write_text(
+        (cmds_dir / "speckit.broken.md").write_text(
             "---\n"
             "description: [unclosed bracket\n"
             "  invalid: yaml: content: here\n"
@@ -430,9 +430,12 @@ def test_skills_install_for_all_agents(self, temp_dir, agent_key):
 
         # Place .md templates in the agent's commands directory
         agent_folder = AGENT_CONFIG[agent_key]["folder"]
-        cmds_dir = proj / agent_folder.rstrip("/") / "commands"
+        commands_subdir = AGENT_CONFIG[agent_key].get("commands_subdir", "commands")
+        cmds_dir = proj / agent_folder.rstrip("/") / commands_subdir
         cmds_dir.mkdir(parents=True)
-        (cmds_dir / "specify.md").write_text(
+        # Copilot uses speckit.*.agent.md templates; other agents use speckit.*.md
+        fname = "speckit.specify.agent.md" if agent_key == "copilot" else "speckit.specify.md"
+        (cmds_dir / fname).write_text(
             "---\ndescription: Test command\n---\n\n# Test\n\nBody.\n"
         )
 
@@ -448,7 +451,100 @@ def test_skills_install_for_all_agents(self, temp_dir, agent_key):
         assert expected_skill_name in skill_dirs
         assert (skills_dir / expected_skill_name / "SKILL.md").exists()
 
+    def test_copilot_ignores_non_speckit_agents(self, project_dir):
+        """Non-speckit markdown in .github/agents/ must not produce skills."""
+        agents_dir = project_dir / ".github" / "agents"
+        agents_dir.mkdir(parents=True, exist_ok=True)
+        (agents_dir / "speckit.plan.agent.md").write_text(
+            "---\ndescription: Generate implementation plan.\n---\n\n# Plan\n\nBody.\n"
+        )
+        (agents_dir / "my-custom-agent.agent.md").write_text(
+            "---\ndescription: A user custom agent\n---\n\n# Custom\n\nBody.\n"
+        )
 
+        result = install_ai_skills(project_dir, "copilot")
+
+        assert result is True
+        skills_dir = _get_skills_dir(project_dir, "copilot")
+        assert skills_dir.exists()
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert "speckit-plan" in skill_dirs
+        assert "speckit-my-custom-agent.agent" not in skill_dirs
+        assert "speckit-my-custom-agent" not in skill_dirs
+
+    @pytest.mark.parametrize("agent_key,custom_file", [
+        ("claude", "review.md"),
+        ("cursor-agent", "deploy.md"),
+        ("qwen", "my-workflow.md"),
+    ])
+    def test_non_speckit_commands_ignored_for_all_agents(self, temp_dir, agent_key, custom_file):
+        """User-authored command files must not produce skills for any agent."""
+        proj = temp_dir / f"proj-{agent_key}"
+        proj.mkdir()
+
+        agent_folder = AGENT_CONFIG[agent_key]["folder"]
+        commands_subdir = AGENT_CONFIG[agent_key].get("commands_subdir", "commands")
+        cmds_dir = proj / agent_folder.rstrip("/") / commands_subdir
+        cmds_dir.mkdir(parents=True)
+        (cmds_dir / "speckit.specify.md").write_text(
+            "---\ndescription: Create spec.\n---\n\n# Specify\n\nBody.\n"
+        )
+        (cmds_dir / custom_file).write_text(
+            "---\ndescription: User custom command\n---\n\n# Custom\n\nBody.\n"
+        )
+
+        result = install_ai_skills(proj, agent_key)
+
+        assert result is True
+        skills_dir = _get_skills_dir(proj, agent_key)
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert "speckit-specify" in skill_dirs
+        custom_stem = Path(custom_file).stem
+        assert f"speckit-{custom_stem}" not in skill_dirs
+
+    def test_copilot_fallback_when_only_non_speckit_agents(self, project_dir):
+        """Fallback to templates/commands/ when .github/agents/ has no speckit.*.md files."""
+        agents_dir = project_dir / ".github" / "agents"
+        agents_dir.mkdir(parents=True, exist_ok=True)
+        # Only a user-authored agent, no speckit.* templates
+        (agents_dir / "my-custom-agent.agent.md").write_text(
+            "---\ndescription: A user custom agent\n---\n\n# Custom\n\nBody.\n"
+        )
+
+        result = install_ai_skills(project_dir, "copilot")
+
+        # Should succeed via fallback to templates/commands/
+        assert result is True
+        skills_dir = _get_skills_dir(project_dir, "copilot")
+        assert skills_dir.exists()
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        # Should have skills from fallback templates, not from the custom agent
+        assert "speckit-plan" in skill_dirs
+        assert not any("my-custom" in d for d in skill_dirs)
+
+    @pytest.mark.parametrize("agent_key", ["claude", "cursor-agent", "qwen"])
+    def test_fallback_when_only_non_speckit_commands(self, temp_dir, agent_key):
+        """Fallback to templates/commands/ when agent dir has no speckit.*.md files."""
+        proj = temp_dir / f"proj-{agent_key}"
+        proj.mkdir()
+
+        agent_folder = AGENT_CONFIG[agent_key]["folder"]
+        commands_subdir = AGENT_CONFIG[agent_key].get("commands_subdir", "commands")
+        cmds_dir = proj / agent_folder.rstrip("/") / commands_subdir
+        cmds_dir.mkdir(parents=True)
+        # Only a user-authored command, no speckit.* templates
+        (cmds_dir / "my-custom-command.md").write_text(
+            "---\ndescription: User custom command\n---\n\n# Custom\n\nBody.\n"
+        )
+
+        result = install_ai_skills(proj, agent_key)
+
+        # Should succeed via fallback to templates/commands/
+        assert result is True
+        skills_dir = _get_skills_dir(proj, agent_key)
+        assert skills_dir.exists()
+        skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
+        assert not any("my-custom" in d for d in skill_dirs)
 
 class TestCommandCoexistence:
     """Verify install_ai_skills never touches command files.
@@ -460,14 +556,16 @@ class TestCommandCoexistence:
 
     def test_existing_commands_preserved_claude(self, project_dir, templates_dir, commands_dir_claude):
         """install_ai_skills must NOT remove pre-existing .claude/commands files."""
-        # Verify commands exist before
-        assert len(list(commands_dir_claude.glob("speckit.*"))) == 3
+        # Verify commands exist before (templates_dir adds 4 speckit.* files,
+        # commands_dir_claude overlaps with 3 of them)
+        before = list(commands_dir_claude.glob("speckit.*"))
+        assert len(before) >= 3
 
         install_ai_skills(project_dir, "claude")
 
         # Commands must still be there — install_ai_skills never touches them
         remaining = list(commands_dir_claude.glob("speckit.*"))
-        assert len(remaining) == 3
+        assert len(remaining) == len(before)
 
     def test_existing_commands_preserved_gemini(self, project_dir, templates_dir, commands_dir_gemini):
         """install_ai_skills must NOT remove pre-existing .gemini/commands files."""