Add data source filenames and directories to CytoTable metadata (or similar)

CytoTable attempts to keep track of source data filenames using dictionary and list structures (depending on the output type). This issue focuses on moving that metadata to, for example, CytoTable metadata inside the output file(s). It may also be there are opportunities to store this data within the columns or values themselves.

Start by tracing where CytoTable currently stores source data filenames in dictionaries and lists for each output type. Compare the available output metadata structures and determine whether filenames and directories should live in file metadata, columns, or values. Done means the chosen metadata location consistently preserves this source information across the affected outputs.

Written by the indexing model from the issue text.