Cleanup after workspace refactoring

[JannikStreek]

After https://github.com/ether/etherpad-lite/issues/6166 some tasks remain open:

• [x] Cleanup comments, e.g. in docker build file, as these are now outdated and refer to old commands
• [x] node_modules directory in the root folder should be mapped to a value as pnpm hoists dependencies there
• [x] move bin folder one level up. it doesn't make sense anymore to have it in the src folder