[FIX] Makes pair_align compile on travis.

This PR allows pair_align to be compiled on Travis again.
Features:
   * Split pair_align into multiple translation units.
   * There is one staticlibrary for lcs, local and all 16 global alignments (All possible AlignConfig configurations).
   * The libs are built in a separate lib folder and linked into a global library, which is then pair_align links against.

Note, with cmake 2.8.8. we could use the ```OBJECT``` feature for ```add_library```, which only builds object files instead of linking every source file into a library. This is documented in the CMakeLists.txt
This would go away if you merge the two loops.