fix: harden autonomy dashboard and obsidian integration

Author: Aitomates

universal-refiner/.gemini-refiner.example.json

@@ -1,5 +1,5 @@
 {
-  "_comment_usage": "Copy this file to .gemini-refiner.json and fill in your values. This file is safe to commit.",
+  "_comment_usage": "Legacy example only. Prefer .universal-refiner.example.json and copy that file to .universal-refiner.json. This file is safe to commit.",
   "_comment_fields": "All fields are optional. Omit a section to use built-in defaults.",
   "semantic": {
     "_comment": "Configure the local OpenAI-compatible provider (Ollama, LM Studio, etc.)",

universal-refiner/package-lock.json

@@ -45,20 +45,20 @@
     "dependencies": {
         "@hono/node-server": "^1.19.13",
         "@modelcontextprotocol/sdk": "^1.29.0",
+        "@lancedb/lancedb": "^0.30.0",
         "better-sqlite3": "^12.8.0",
+        "chokidar": "^5.0.0",
+        "flexsearch": "^0.8.212",
         "hono": "^4.12.25",
         "typescript": "^5.9.3",
         "zod": "^4.3.6"
     },
     "devDependencies": {
         "@emnapi/core": "^1.11.1",
         "@emnapi/runtime": "^1.11.1",
-        "@lancedb/lancedb": "^0.30.0",
         "@types/better-sqlite3": "^7.6.13",
         "@types/node": "^22.19.17",
         "@vitest/coverage-v8": "4.1.4",
-        "chokidar": "^5.0.0",
-        "flexsearch": "^0.8.212",
         "ts-node": "^10.9.2",
         "vitest": "^4.1.4"
     },