I and Ivan Levkivskyi are planning to start implementing a switch to a modular typeshed. This will involve a new directory structure for typeshed. All tools that use typeshed will likely require some changes.
Here's the announcement: https://github.com/python/typeshed/issues/2491#issuecomment-758751253
We discussed the plan last spring at typeshed, but the implementation got delayed until now.
Let's continue the discussion in the above GitHub issue. It also contains the full proposal + incremental updates in additional comments.