Setup reading map files from a user provided directory

This MR changes how map files in EFTracking FPGASim are setup. In the past we assumed some fixed dir on CVMFS. Now this dir is made fully confiurable. This will likely change in the future and we'll go back to CVMFS but for next phase this is optimal.

There is several other small updates that were needed to get map gen + running from wrapper files possible. Also updates to the doc.

taggin @kazheng @jahreda