WIP: fix directory targets with empty subdirs

[ElectreAAS]

This PR is related to... a lot of things actually.

For some context, let's take this test file from #11116 & #11117:
Why isn't the empty directory output/child restored from cache like output/file?

• is it because a directory has a name that dune doesn't like, as in [regression] promotion of directory targets has trouble with directories starting in @ #10609?
• is it because it's too deep in a directory target, as in Failure in promote mode for directory targets with subdirectories #11214?
• or the same thing, but different, as in [fix] [directory targets] Fix promotion of directory targets in some cases #10931?
• also why doesn't Fix promotion of directory targets without files in them #11203 fix that too?

I'm not really sure, and the original author of this piece of code (rleshchinskiy) doesn't seem very active in this project at this time.
What I am sure of is that breaking the logic of collect is easy to do accidentally, but that at least fixes one problem.

Debugging this is tricky, as a lot of tests fail with a cryptic

Error: Is a directory
-> required by _build/default/a
[1]

I'll note however that the problems likely originates in either #9407, #9470, or #9535.

[ElectreAAS]

cc-ing the entire planet for good measure, but don't feel obligated to participate (it's the holiday season after all 😃)

@maiste @rgrinberg @rleshchinskiy @snowleopard @moyodiallo @mefyl @ejgallego

[ElectreAAS]

Belated update before the holidays:
I changed the internal representation of targets (Targets.Produced.t) to be hierarchical - it felt like the right move to detect broken logic, and was mentioned in the comments as something to be done at some point.
From that change I saw that the 'empty-dir' test passed, but a whole lot of other tests didn't. I thought I could work backwards from that to a point where all would pass, but the explanation was harsh: I had broken the caching mechanism, and the only reason the 'empty-dir' test passed was because nothing was cached and everything was rerun 🤦.
When I finally fixed everything else, obviously the 'empty-dir' test didn't pass (the cache worked like it did before my changes, wow!).
At this point in time I have pushed my changes, and they don't break anything, but also don't fix anything...
My hunch now is that this traversal only stores files as metadata, which means that this entries list only contains metadata about files, which means they're the only things getting restored. I tried making a of_files_plus_dirs to be used at that call site, but couldn't get it to work so far. Also I don't know how to generate digests of empty directories to actually store them in metadata...

Hope this progress report isn't too arcanic for reviewers 🙂