Minor clean up in linear solver
Updated documentations
Documentation for EquelleRuntimeCUDA
Changed struct -> class for consistency.

Avoids compiler warnings with newer compilers.
Turn off more warnings triggered by flex-generated code.
Fix a bug and use EXTRA... variables for cmake.
Suppress compile warnings.
Remove include dirs from link_directories() command.
Silence warning in bdyfaces.cpp.
Updated examples.

Mostly for easier legibility with narrow screen width (for presentations),
but also some clarifications, comment fixes and re-ordering of code fragments.