fix(CMakeLists.txt): clean up external dir structure; use NDEBUG for gflag
fix(util/git_sha1): add copyright, wrap with namespace
fix(main): cmd-line parsing

 - move cmd-line parsing from SMTConfig to main.
 - run gflags first, update argc and argv. Then call SMTConfig with the
   updated ones.
 - check whether a given file exists or not.

This closes dreal/dreal#39