adds missing cc
nicer gitignore

with help from https://github.com/github/gitignore.git
Indentation to make code more readable
Added missing include
Whitespace/docu changes
more file splitting
split hmm/elliptic_hmm_matrix_assembler.hh
more file splitting
potentially re-enable building with autofools
fix gcc 4.7 compile
more gcc 4.7 fixes