- The Basys 3 has non-inverted LEDs, thus we need to set the G_LED_ON
   generic.
 - The top_module needs to be set with the base name only.
 - Also, remove 2nd stage Synplify project.

 - show maximum polynomial for current LFSR width in tooltip
 - set maximum polynomial when changing LFSR width

Previously, FIJI Setup told the user only that some nets in the settings
file do not match the supplied netlist but did not state their names.
This patch adds this output to the log and GUI dialogs.

Also, fix some indentions.

Also, do not repeat warnings as errors in GUIs and during instrumentation.

 - links to footnotes were fixed by deferring the loading of hyperref until
   after footmisc.
 - some cross-document links were wrong

* Created a method for updating all warning indicators next to the Tab names
* Corrected behavior when the FIUs indicator is on and the causing FIU is deleted

* Segfault when deselecting all nets
* When a net entry was empty (" "), the user first had to de-select this net

New feature branch: allow selection of multiple nets in FIU tab. Automatically creates FIUs for selected nets

The correct full command line should have been:

find * -type f \( -name "*.pm" -or -name "*.pl" -or -name "*.tst" -or -name "*.cfg" -or -name "*.vhd" -or -name "*.psl" -or -name "*.do" \) -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'

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