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]

Update before the week-end (I'll refine this on monday):
Changed the internal representation to be hierarchical - it feels like the right move to detect broken logic, but I'm not 100% convinced.
Left some fun comments for reviewers, and a fair amount of printing stuff

Note that the changed test 'empty-dir' actually passes (besides the printing), but the added one 'subdirs-only' fails like those in the CI.