Add version numbering to preprocessing

Vendor's don't necessarily store version information in their file formats. Add a version parameter to future-proof preprocessing.

Start by locating the preprocessing entry point and reviewing how file-format information is currently handled. Determine where a version parameter would be passed and stored, then define the expected behavior for formats that do and do not provide version information. Done means preprocessing can preserve or accept version information without breaking existing inputs.

Written by the indexing model from the issue text.