Yara supports more / longer contigs

To implement this feature humanly, I had to change the FMIndexConfig object (see 42ee6e4, 65fcb35).

Unfortunately this change breaks the compilation of the CUDA FMIndex and would require a rework of the device types propagation mechanism (which is inhuman). Apart from that, tests already fail with CUDA 5.5 and probably don't even compile with CUDA >= 6.0. @weese which version is used on stinger? Both 5.5 and 6.0 are installed...

I also fixed and improved various basic SeqAn types (see c86fe71 to 7dec75c).