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chore: Remove extraneous files, fix small issues in README#11

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CalebLarsen wants to merge 1 commit intoWaymentSteeleLab:masterfrom
CalebLarsen:tidy_repo
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chore: Remove extraneous files, fix small issues in README#11
CalebLarsen wants to merge 1 commit intoWaymentSteeleLab:masterfrom
CalebLarsen:tidy_repo

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I removed some files that shouldn't be in the repo like a build of score_prediction, an unofficial testing file tmp.seq and some hidden files. I also fixed a couple of things in README.md like a typo, one of the links that was broken, and fixed the name of a variable that had changed (C_MIN_HP_LENGTH -> C_MIN_HAIRPIN_LENGTH).

I removed some files that shouldn't be in the repo like a build of
`score_prediction`, an unofficial testing file `tmp.seq` and some hidden
files. I also fixed a couple of things in `README.md` like a typo, one
of the links that was broken, and added bash syntax highlighting to the
relevant example commands.
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