chore(paths): refactor data directory structure and update references

- Updated paths for instance data, workflows, and logs to use a unified `data/` directory.
- Adjusted related documentation in AGENTS.md and README.md to reflect the new data structure.
- Refactored path handling in server files to ensure consistency and clarity in data management.
- Enhanced test scripts to align with the new directory structure for improved organization.

packages/server/pm2-bridge.js

@@ -1,8 +1,6 @@
 import path from "path";
 import pm2 from "pm2";
-import { SERVER_ROOT } from "./paths.js";
-
-const REPO_ROOT = path.resolve(SERVER_ROOT, "../..");
+import { REPO_ROOT, SERVER_ROOT } from "./paths.js";
 
 export const PM2_HTTP_NAME = "jflow-http";
 export const PM2_WORKER_NAME = "jflow-worker";