in recon/ directory:
treetest/ contains code to apply some cuts and write a new tree to recon/tree/
cuts/ contains code to apply cuts to the new tree
hist/ contains code to plot histograms from data in the new tree

All main files in these are called analysis.C, as they were all copy and pasted from the same initial cmt thing. 

cut functions which have been made so far are in a separate cuts.C with a cuts.h, these files are in the cuts/ tree and linked to from treetest/