Also, change cross-document reference to look for the "other" pdf
file in the current directory instead of ../dir-name/

And some other minor refinements

find * -type f \( -name "*.pm" -or -name "*.pl" -or -name "*.tst" -or -name "*.cfg" \) -print0 | parallel -q -0 sed -i -e 's/FAULT_DETECT_/FD_/g;s/RESET_/RST_/g;s/TRIGGER_/TRIG_/g;s/INSTRUMENTATION_/INST_/g;s/IMPLEMENTATION_/IMPL_/g;s/_DURATION/_DUR/g;s/_ACTIVE/_ACT/g;s/_CONFIG/_CFG/g;s/OPTIMIZATION_OFF/OPT_OFF/g;s/s_fiji_trigger_/s_fiji_trig_/g'

 - cover page:
    * remove explicit copyright notice
    * add same acknowledgment as in papers
 - use a single main makefile
 - move together common images
 - set image search path to common_tex/img
 - include a unified tex header file

Due to the weird level mechanism of Log4Perl the we cannot (easily)
set the verbosity directly but only increase it. Rename functions and
variables to reflect this better and use the new function correctly.