uses top_srcdir instead of top_builddir for bundled scotch directory; cleans up code a bit
parameters string length increased to 512.
Merge remote-tracking branch 'upstream/devel' into devel

Conflicts:
	src/shared/read_value_parameters.f90
ignore latex generated files for doc
Merge branch 'QA' of https://github.com/geodynamics/specfem3d into devel
updates configuration scripts to allow for building binaries in a different directory than the root directory; bug fix in check_mesh_resolution() which speeds it up; adds middle abscissa check into zwgldj() routine and removes the checks in other locations
adds subdirectory tests/ for compilation and unit testing; deallocates temporary arrays in check_valence(); uses cudaMemcpy2D for padded array copies