Fix includes

[JoshuaSBrown]

Changed system includes to local includes, this prevents issues that occur during compile time. E.g. if a header file is deleted in a new pull request but the header file is included in some of the source files in the pull request. In such a case, no errors will be seen if tested locally as the compiler will still find the file in the system includes. By building with what is in the local repo you avoid false positive builds.

[codecov]

Codecov Report

Merging #487 into master will not change coverage.
The diff coverage is n/a.

@@          Coverage Diff           @@
##           master    #487   +/-   ##
======================================
  Coverage    61.1%   61.1%           
======================================
  Files         129     129           
  Lines        6322    6322           
======================================
  Hits         3869    3869           
  Misses       2453    2453

Flag	Coverage Δ
#gcc	61.1% <ø> (ø)	⬆️

Impacted Files	Coverage Δ
src/libcsg/version.cc	100% <ø> (ø)	⬆️
src/tools/csg_fmatch.cc	79.1% <ø> (ø)	⬆️
src/csg_boltzmann/tabulatedpotential.cc	62.9% <ø> (ø)	⬆️
src/tools/csg_fmatch.h	100% <ø> (ø)	⬆️
src/tools/csg_stat.cc	100% <ø> (ø)	⬆️
src/libcsg/modules/io/xyzreader.cc	4.3% <ø> (ø)	⬆️
src/tools/csg_gmxtopol.cc	21.3% <ø> (ø)	⬆️
src/libcsg/nematicorder.cc	3.2% <ø> (ø)	⬆️
src/libcsg/topologyreader.cc	100% <ø> (ø)	⬆️
src/libcsg/modules/io/gmxtopologyreader.h	100% <ø> (ø)	⬆️
... and 62 more

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