Repo cleanup

[jmtsuji]

Several scripts in this repo now have limited use or are deprecated:

• fastx_subset.sh: can be done in a straightforward way using xargs/parallel and seqtk, so I think this script is no longer needed.
• predict_short_orfs.sh: now that FragGeneScanRS is available, I don't think this wrapper is needed anymore. The reformat logic is still kind of helpful but is really just a code snippet and might not need its own script
• check_md5_hashes.sh: I personally don't think I have used this script in years; is it really needed? A short for loop could be written whenever the need arises.

Might it be reasonable to remove these from the repo, for decluttering purposes?