Integration tests

This pull request creates our first integration test, confirming that the distance travelled by the tetrahedral complex over 30 seconds remains consistent over time. The value is only slightly different from what we reported in the 6WCSCM paper. The following changes were required to make this happen:

1) Moving the files required by and written to by learning into the resources folder (only done for the applications in examples)
2) Updating AnnealAdapter so it can read from the resources folder. It will still look for a local logs file by default. BaseSpineCPGControl was also updated to use these options.
3) Adding two more options to bin/build.sh so the integration tests mirror the unit tests.