chore: standardize repo setup files

.prettierignore

@@ -1,24 +1,14 @@
 build
 coverage
 dist
+node_modules
+package-lock.json
+
 dist-ssr
 release
-
-node_modules
-src/mcp-server/node_modules
-package-lock.json
-pnpm-lock.yaml
-yarn.lock
-
 db
-
-.env
-
 *.min.js
 *.min.css
 openapi.json
-
-# Generated by drizzle-kit; formatting is the tool's own
 drizzle/
-
 src/ui/settings/settings-search-index.ts