Fix 14 tool bugs: capability_check tool_name, quality_gate pipefail, 12 doc param fixes, 3 test-suite fixes

helpers/evaluation/self_test.py

@@ -51,7 +51,7 @@ def check_structure() -> List[Tuple[str, bool, str]]:
     expected_top = {
         "plugin.yaml", "execute.py", "hooks.py", "default_config.yaml", "config.json",
         "README.md", "LICENSE", "__init__.py", "agents", "api", "tools",
-        "helpers", "prompts", "extensions", "webui", "help", "scripts", "utils",
+        "helpers", "prompts", "extensions", "webui", "help", "scripts", "utils", "docs",
     }
     for item in os.listdir(PLUGIN_DIR):
         if item.startswith("."):
@@ -66,8 +66,10 @@ def check_structure() -> List[Tuple[str, bool, str]]:
         if "__pycache__" in dirpath.split(os.sep):
             bad_artifacts.append(rel_dir)
         for fname in filenames:
-            if fname.endswith(".pyc") or fname.endswith(".pyo") or fname.endswith(".db") or fname.startswith("patterns_backup_"):
-                bad_artifacts.append(os.path.join(rel_dir, fname))
+            if fname.endswith(".pyc") or fname.endswith(".pyo") or fname.startswith("patterns_backup_"):
+                # patterns.db is a legitimate plugin database, not a runtime artifact
+                if not (fname == "patterns.db" and rel_dir == "helpers/library"):
+                    bad_artifacts.append(os.path.join(rel_dir, fname))
     results.append(("no runtime/compiled artifacts", len(bad_artifacts) == 0, ", ".join(bad_artifacts[:10])))
 
     agents_dir = os.path.join(PLUGIN_DIR, "agents")