Improve CLI: config store, heartbeat-run, and onboarding

Rework config store with better file handling. Expand heartbeat-run
command with richer output and error reporting. Improve configure
and onboard commands. Update doctor checks.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

package.json

@@ -12,7 +12,7 @@
     "test:run": "vitest run",
     "db:generate": "pnpm --filter @paperclip/db generate",
     "db:migrate": "pnpm --filter @paperclip/db migrate",
-    "paperclip": "tsx cli/src/index.ts"
+    "paperclip": "node cli/node_modules/tsx/dist/cli.mjs cli/src/index.ts"
   },
   "devDependencies": {
     "typescript": "^5.7.3",