Refactor `clone` package

[carreter]

Per @Koeng101 's suggestion, the clone package needs some refactoring to make its code easier to understand and use.

Blocks #359 .

[github-actions]

This issue has had no activity in the past 2 months. Marking as stale.

[carreter]

Reopening this because the clone package still needs a good amount of work. Thinking of spending a significant amount of time on this during the first half of January, as most of the scripts I will be writing for Prof. Weiss' lab will be related to cloning.

@TwFlem would love to get your input on what you think needs to be done. You mentioned seqhash needing some optimization - I bet we could just look at recently published algos and make our own implementation. I'd also like to rewrite the structs that hold the data on DNA parts/fragments to make them more flexible and properly encode 3' vs 5' overhangs.