Add readme generation

• Added README generation.

• Refactor code.

Bug fix for error when no overlapping embeddings

• Bug fix: raise more informative error when no embeddings overlap.

Added provenance flag

• Added --provenance flag to pass a path to json file with provenance information. This removes the
  necessity of input directory to be an RO-Crate.

Added new coembedding algorithm

• Added a new coembedding algorithm accessible via flag --algorithm auto. This algorithm utilizes neural networks
  to generate latent embeddings, optimizing both reconstruction and triplet losses to improve embedding accuracy
  by learning intra- and inter-modality relationships.

First release

• First release