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old location, corrects some accesses of reference FASTAs (where the `fasta_file` accessor might return a path that is no longer valid), and cleans up a few things along the way.
In places like this where we are providing helpful example values in documentation, should we instead just provide a lister command that can be executed to provide the current refseq build and its fasta file? I suppose this is not perfect either as it is subject to change but perhaps it's slightly less subject to change? I'm unsure. It also requires the user to run something rather than simply look at --help.