Remove References to /gscmnt/839

/gscmnt/839 is being decommissioned.

This updates examples that were pointing to it to point to the new location of the same file/directory, removes some defaults that were pointing to the old location, corrects some accesses of reference FASTAs (where the `fasta_file` accessor might return a path that is no longer valid), and cleans up a few things along the way.
It might be better; I'm not sure I want lister commands littered throughout the codebase either.  Perhaps we could have a "how to find a reference FASTA" tutorial somewhere?  Given your +1, I will merge this PR for now, since time is short before these volumes disappear, but we can/should keep discussing better options.