I'm using filesystem more as a metaphor than literally.

I picked this metaphor because "apps" are many-to-many to "file formats". I found "file format" to be a very powerful analogy for lexicons so I kind of built everything else in the explanation around that.

You can read https://atproto.com/specs/repository for more technical details about the repository data structure:

The repository data structure is content-addressed (a Merkle-tree), and every mutation of repository contents (eg, addition, removal, and updates to records) results in a new commit data hash value (CID). Commits are cryptographically signed, with rotatable signing keys, which allows recursive validation of content as a whole or in part. Repositories and their contents are canonically stored in binary DAG-CBOR format, as a graph of data objects referencing each other by content hash (CID Links). Large binary blobs are not stored directly in repositories, though they are referenced by hash (CID).

Re: apps, I'd say AT is actually post-app to some extent because Lexicons aren't 1:1 to apps. You can share Lexicons between apps and I totally can see a future where the boundaries are blurring and it's something closer to what you're describing.