Add all-in-one pairwise alignment wrapper

[trivoldus28]

Example CUE that I actually used provided. Generally ready for review, except mypy and I'm not sure if it's worth it? For the event of excluding it from mypy, I wasn't sure if there's a option to do that or to move the file to internal.

Also looking for feedback on how things can be different for usability. In the example, the idea is that to adapt to different project the user only has to modify the first 150 lines. Everything else (like manipulating paths) should be as automated as possible to remove fluffs and improve readability.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (9295d11) to head (c1f2663).
Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #650   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files          128       128           
  Lines         4572      4527   -45     
=========================================
- Hits          4572      4527   -45     

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[trivoldus28]

Since it's likely to need significant work to get it pass tests, I'll make it draft for now and revisit it later next time I use it.