Improve identification of BIDS data files and sidecars

[clane9]

Fixes issues of mis-identifying BIDS data files and JSON sidecars brought up in #36.

• Multiple non-sidecar JSONs in a session directory incorrectly treated as sidecars due to bad file matching.
• Compound JSON extensions like '.surf.json' incorrectly treated as sidecars.
• Missing directories such as microscopy '.ome.zarr' directories and MEG '.ds' directories.
• Incorrectly including files contained in the above directories.
• Incorrectly including metadata files like '*_scans.tsv'.