chore(deps): update pnpm version and clean up package.json; remove unused dependencies and scripts

- Updated package manager to pnpm@11.22.0 in package.json.
- Removed unused dependencies and scripts from package.json and pnpm-lock.yaml.
- Cleaned up fs-store.js and other files by removing commented-out code and unused imports.
- Updated workflow configurations to use environment variables for URLs.

pnpm-workspace.yaml

@@ -2,4 +2,8 @@ packages:
   - packages/*
 allowBuilds:
   better-sqlite3: true
+  cpu-features: true
   esbuild: true
+  msgpackr-extract: true
+  ssh2: true
+  rss-parser: true