Remove use of boost::filesystem and boost::optional

[jslee02]

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• Document new methods and classes
• Format new code files using ClangFormat by running make format
• Build with -DDART_TREAT_WARNINGS_AS_ERRORS=ON and resolve all the compile warnings

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[codecov]

Codecov Report

Merging #1648 (292938d) into main (2a158b1) will increase coverage by 0.00%.
The diff coverage is 75.00%.

@@           Coverage Diff           @@
##             main    #1648   +/-   ##
=======================================
  Coverage   59.13%   59.13%           
=======================================
  Files         497      497           
  Lines       40881    40881           
=======================================
+ Hits        24174    24175    +1     
+ Misses      16707    16706    -1     

Impacted Files	Coverage Δ
dart/utils/mjcf/detail/Body.cpp	81.25% <ø> (ø)
dart/utils/mjcf/detail/Body.hpp	100.00% <ø> (ø)
dart/utils/mjcf/detail/BodyAttributes.cpp	67.34% <ø> (ø)
dart/utils/mjcf/detail/Compiler.cpp	47.70% <ø> (ø)
dart/utils/mjcf/detail/Geom.cpp	70.94% <ø> (ø)
dart/utils/mjcf/detail/Inertial.hpp	100.00% <ø> (ø)
dart/utils/mjcf/detail/Site.cpp	41.57% <ø> (ø)
dart/utils/mjcf/detail/Site.hpp	100.00% <ø> (ø)
dart/utils/mjcf/detail/Utils.cpp	61.70% <ø> (ø)
dart/utils/mjcf/detail/Weld.hpp	100.00% <ø> (ø)
... and 7 more