bugfix: don't exit the syst loop when failing flags

This bug was the reason for the large systematic uncertainties
(the last three ones JER, SCALEST_UP, SCALEST_DN, RESOST).
See details in the email "Sys for cross check" 2014-03-20.
debugging 179974
cmd: update hft in/out dirs
check_hft_trees: add msg before fail
check_hft_trees: put back all samples (done debugging?)
convert to makefile (under test)