Add unaligned FASTA input type

[priyappillai]

In design.py:

• Move --mafft-path and --cluster-threshold to the base subparser
• Add --unaligned to fasta subparser
• Add --write-input-aln to fasta subparser
• Change --write-input-seqs to also be a prefix to a path, to match other inputs (unrelated, sneaking in here)
• Modify processing to account for above changes (mostly in prepare_alignments())

In prepare_alignment.py:

• Allow for no reference accessions (necessary for unaligned FASTA input type)

[codecov[bot]]

Codecov Report

Merging #58 (c09f397) into main (524cadc) will increase coverage by 0.32%. The diff coverage is 66.66%.

@@            Coverage Diff             @@
##             main      #58      +/-   ##
==========================================
+ Coverage   84.83%   85.15%   +0.32%     
==========================================
  Files          48       48              
  Lines        7543     7599      +56     
==========================================
+ Hits         6399     6471      +72     
+ Misses       1144     1128      -16     

Impacted Files	Coverage Δ
bin/design.py	65.81% <50.00%> (+1.59%)	:arrow_up:
adapt/prepare/prepare_alignment.py	63.63% <83.33%> (+9.03%)	:arrow_up:
bin/tests/test_design.py	99.51% <100.00%> (+1.16%)	:arrow_up:

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[priyappillai]

On the Codecov report-I don't think all of the differences are super necessary to be tested? I can at least add basic tests for the unaligned fasta input type to our integration tests. Also can modify Codecov to just comment and not do the "check".