Particle Gun fix, Updated CKF

Sim changes:

• Fix setting of particle gun parameters so they actually are used
• Create proper uniform phase space sampling over a radius
• Update config files for these changes

Digi changes:

• Create digi/merge script to handle small hits files

Reco changes:

• Merge Tobias CKF2 update
• Set up to use material corrections file (now on cvmfs)
• Write raw tracker hits and MC truth in reco output
• Change waveform timing threshold to 40% (optimal value)