Fix clang and removed unneeded headers

[MFraters]

This is a follow up for #293 and related to issue #294. Clean up header files with IWYU and custom script (which can be found here: https://stackoverflow.com/a/7135530) which goes through all the files and removes the includes one by one. This is has been a bit messy and a lot of checking and fixing by hand, but the final result is an improvement. So I am not going to include the codes I used to do this in the pull request for now.

[codecov]

Codecov Report

Merging #295 (16142c5) into master (bdb5458) will not change coverage.
The diff coverage is 100.00%.

❗ Current head 16142c5 differs from pull request most recent head f50d0c6. Consider uploading reports for the commit f50d0c6 to get more accurate results

@@           Coverage Diff           @@
##           master     #295   +/-   ##
=======================================
  Coverage   99.00%   99.00%           
=======================================
  Files          74       74           
  Lines        4228     4228           
=======================================
  Hits         4186     4186           
  Misses         42       42           

Impacted Files	Coverage Δ
app/main.cc	97.43% <ø> (ø)
source/coordinate_systems/cartesian.cc	100.00% <ø> (ø)
source/coordinate_systems/interface.cc	100.00% <ø> (ø)
source/coordinate_systems/spherical.cc	100.00% <ø> (ø)
source/features/continental_plate.cc	100.00% <ø> (ø)
.../continental_plate_models/composition/interface.cc	100.00% <ø> (ø)
...es/continental_plate_models/composition/uniform.cc	100.00% <ø> (ø)
...tures/continental_plate_models/grains/interface.cc	100.00% <ø> (ø)
...plate_models/grains/random_uniform_distribution.cc	100.00% <ø> (ø)
...eatures/continental_plate_models/grains/uniform.cc	100.00% <ø> (ø)
... and 64 more

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[github-actions]

Benchmark	Master	Feature	Difference (99.9% CI)
Slab interpolation simple none	1.547 ± 0.053 (s=304)	1.546 ± 0.052 (s=281)	-1.0% .. +0.8%
Slab interpolation curved simple none	1.613 ± 0.040 (s=291)	1.621 ± 0.038 (s=268)	-0.2% .. +1.1%
Spherical slab interpolation simple none	2.172 ± 0.023 (s=205)	2.177 ± 0.019 (s=211)	-0.1% .. +0.5%
Slab interpolation simple curved CMS	1.780 ± 0.003 (s=258)	1.791 ± 0.004 (s=249)	+0.6% .. +0.7%
Spherical slab interpolation simple CMS	4.192 ± 0.065 (s=101)	4.198 ± 0.082 (s=116)	-0.6% .. +1.0%
Spherical fault interpolation simple none	2.641 ± 0.078 (s=172)	2.650 ± 0.076 (s=171)	-0.7% .. +1.4%