Try to improve clang-tidy runtimes

[reedacartwright]

Add a .clang-tidy-ignore and .clang-tidy-include files.

Remove and rearrange #include lines to reduce the amount of unused headers included in files.

Partially fixes #13

[codecov-commenter]

Codecov Report

Patch coverage: 89.28% and project coverage change: +0.22 🎉

Comparison is base (cd2700e) 90.00% compared to head (526733b) 90.22%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #21      +/-   ##
==========================================
+ Coverage   90.00%   90.22%   +0.22%     
==========================================
  Files          24       25       +1     
  Lines        1721     1709      -12     
  Branches      911      904       -7     
==========================================
- Hits         1549     1542       -7     
+ Misses         49       47       -2     
+ Partials      123      120       -3     

Impacted Files	Coverage Δ
src/include/coati/align_pair.hpp	100.00% <ø> (ø)
src/include/coati/dna_syms.hpp	2.73% <ø> (ø)
src/include/coati/semiring.hpp	100.00% <ø> (ø)
src/include/coati/structs.hpp	75.00% <ø> (+2.27%)	⬆️
src/lib/align_fst.cc	100.00% <ø> (ø)
src/lib/align_marginal.cc	85.83% <ø> (ø)
src/lib/fasta.cc	90.24% <ø> (ø)
src/lib/json.cc	92.50% <ø> (ø)
src/lib/mutation_fst.cc	98.16% <ø> (ø)
src/lib/phylip.cc	94.64% <ø> (ø)
... and 8 more

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