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:
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.