Consider a separate directory for reference files

Currently in the file structure for `scRNA-seq`, we have some reference files (eg mitochondrial genes) that hang out in `data/` directories, but these aren't exactly data! It would be a bit of a lift to overhaul this, but we might consider having a somewhat different structure for these files and placing them into a separate `reference_files/` directory.

Review the scRNA-seq module's current data/ directories and inventory reference files such as mitochondrial-gene lists. Define the scope and target structure for moving them into reference_files/; done means the affected references are consistently organized without breaking module paths.

Written by the indexing model from the issue text.