Fix mismatched include guards, remove deprecated register specification, switch from unnamed to named POSIX semaphore, as unnamed semaphores are deprecated and unsupported on OS X
Add necessary semaphore/fcntl includes to system_sema.h.  Add c++98/c++11 checking to auto/unique ptrs in gff_stream.h
Add proposed fix to seqan build problems under os x 10.10; untested on prior versions
Merge pull request #646 from ged-lab/test/fix_seqan_warns

Test/fix seqan warns