Add tsk_treeseq_decode_alignments

[benjeffery]

Fixes #3319

Here's a first stab at the C API for alignments. For cleanliness I am using two separate iterations over the tree sequence. It is possible to do it in one, but only by moving the tree owned by the variant decoder, which, while doable, has a bad smell.

[codecov]

Codecov Report

❌ Patch coverage is 65.68627% with 35 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.71%. Comparing base (488b02b) to head (b003a1f).

Files with missing lines	Patch %	Lines
c/tskit/genotypes.c	65.68%	17 Missing and 18 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3324      +/-   ##
==========================================
- Coverage   89.80%   89.71%   -0.09%     
==========================================
  Files          29       29              
  Lines       31062    31164     +102     
  Branches     5687     5718      +31     
==========================================
+ Hits        27894    27960      +66     
- Misses       1779     1796      +17     
- Partials     1389     1408      +19     

Flag	Coverage Δ
c-tests	86.70% <65.68%> (-0.15%)	⬇️
lwt-tests	80.38% <ø> (ø)
python-c-tests	87.05% <ø> (ø)
python-tests	98.84% <ø> (ø)
python-tests-no-jit	33.55% <ø> (ø)
python-tests-numpy1	50.10% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
c/tskit/trees.c	90.99% <ø> (ø)
c/tskit/genotypes.c	80.22% <65.68%> (-4.27%)	⬇️

... and 1 file with indirect coverage changes

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