Test on-the-fly query; fix bugs; add e2e build test

[luciaquirke]

• Add support for module-wise queries
• Basic query tests
• Fix partial run directory rename (shutil is more robust and will handle name collisions by saving the partial directory inside the complete one)
• Fix IndexConfig save to disk
• Add E2E build CLI test
• Fix bug in data batching where it would sometimes go into an infinite loop
• Use Path everywhere

TODO

• Possibly rename module_wise to something more clear
• Don't route indices through the gradient collector, use nonlocal var in collection or something
• Make it more tidy or flexible somehow, right now it's just strategies hard-coded as needed.
  • Separate query gradient transform for unit norm / mean beforehand?
  • Right now we do normalized mean of cosine sims but users might want sum of cosine sims...
• Add better query tests

Follow-up:

• Support alternative query IO for full grads (1-100GB files)
  • If unstructured memmaps are viable we can use them everywhere and provide the structured memmap on request as a view on top of them, no layout change required
• Support module-wise index builds?
• Remove the ScoreWriter ABC if we don't merge the CsvWriter soon, currently we have an abstract class with 1 implementation :')