Test/fix seqan warns

*Fixes the c++11 auto_ptr warnings from seqan
*Fixed several warnings about mismatched include guards
*Changes the unnamed semaphore to a named one, because os x does not (and never has) support(ed) unnamed semaphores.
*Fixed build under os x 10.10, which relies on llvm's libc++ for c++11 support
*Removed "register" keyword, which is deprecated in c++11 and is a non-breaking change