Update for reference writing, parsed filename output

[seasidesparrow]

• enables writing reference files (use -w -r /reference/base/path -s pubabbrev)
• enables output of the parsed filename to the tagged record properties (%I)

Examples:

Parse one delivery of IOP

python run.py -p "/incoming/data/IOPP/**/*.xml" -a 365 -t jats -w -r "/home/data/references/sources/" -s iop -f iop_records.tag -z

Parse one doi, including references

python run.py -d 10.3847/1538-4357/ad0047 -w -s crossref -r "/home/data/references/sources/" -f my_single_doi_record.tag