Command line used was:

find * -type f \( -name "*.pm" -or -name "*.pl" -or -name "*.c" -or -name "*.v" -or -name "*.vhd" -or -name "*.psl" \) -print0 | parallel -q -0 sed -ri -e 's/^([[:blank:]]*[^[:blank:]]+)([[:blank:]]+)(https:\/\/embsys.technikum-wien.at\/projects\/vecs\/fiji)/\1\2\3\n\1\n\1\2The creation of this file has been supported by the publicly funded\n\1\2R\&D project Josef Ressel Center for Verification of Embedded Computing\n\1\2Systems (VECS) managed by the Christian Doppler Gesellschaft (CDG)./g'

For future latency estimation

This includes generated files apart from the instrumented netlist.
The latter just gets a header stating which version of FIJI generated it etc.

Also rename existing licenses to include a .txt suffix and
the license's version.

Even in the case the number of FIUs stored in the settings file (FIU_NUM)
differs from the actual number of FIUs therein, set it to the actual value.
This essential degrades it to a simple size value of the respective fius
array but avoids any confusion in the code.

Before some hash key/value pairs have slipped without being
initialized at all. This caused for example:
"Use of uninitialized value" warnings in FIJITestsViewer.pm line 1137

Does not do what the commit message says at all.

Since there is no way to supply a netlist in FIJI EE it cannot verify anything
related to the netlist, e.g. external port names. However, they are more
or less moot anyway during download because we rely on the design ID
to detect any mismatches between the (actually downloaded) netlist
and the configuration.

Else some hash key/value pairs are not initialized at all.
This causes for example:
"Use of uninitialized value" warnings in FIJITestsViewer.pm line 1137

With this change we also set the defaults unconditionally when loaded
by the GUI. This also requires $global_settings_ref to be passed to
_set_defaults() which was using an inexistent $self->{'settings'} so far.

Also, add some missing strict/warning statements and fix resulting
warnings and refine some comments in the headers of files.

The FIJI version string is stored in the root directory on file VERSION.
This is used in the following places:
 - doxygen uses it as PROJECT_NUMBER (passed as an environment
   variable set by the docs/makefile picked up by the doxyfile)
 - FIJI.pm defines and exports a FIJI_VERSION constant
 - FIJIUtils.pm inserts it for all occurrances of $FIJI_VERSION$ in the about text
 - the UG and TRM show it on their cover pages
 - FIJI/VHDL.pm, Constraints.pm, Netlist.pm put it in all generated files
   (additionally also the design ID is printed where it wasn't before)
 - all "executables" report it in the first log message

Files will be rotated once a day or if they grow to 100 MB up to 7 stages.

 - add new log files to .gitignore
 - refine documentation and install scripts
 - refine log level of "Starting/stopping execution..." to become visible
   in rotated logs
 - minor other log refinements

 - move necessary validation functions into Settings.pm
 - check against FIJI ports too

 - validate nets and respective drivers like everything else
 - load the netlist earlier (in the user scripts) to make it available while
   loading settings
 - add a FIJI::Netlist parameter to respective FIJI::Settings's functions
 - add a new type 'driver' for FIU elements to distinguish its string
   representation from nets'
 - add new net validation function to FIJI::Netlist
 - use this to make net and FIU validation more generic to simplify FIJISettingsViewer
 - refine and correct handling of the tool phases
 - distinguish fatal errors, missing fields and less important anomalies when
   validating settings depending on the phase etc
 - notify user about validation problems in more detailed messages and tooltips
 - refine FIJI::VHDL to not load settings all the time and receive parameters
   directly instead of via hashes
 - use a global constant ONLY_LOAD in fiji_setup instead of a local variable
 - add a 'show_warning' function to ease opening warning dialogs
 - various other usability/GUI-related improvements
 - allow the deletion of nets

Addresses issue vecs/fiji#39

 - extract _add_driver_radiobutton_list from existing code
 - refactor it to allow it to be called repeatedly while reusing widgets
 - make some private Netlist functions public as they are used elsewhere :/
 - eliminate duplicated nets (low-hanging workaround) for a nuisance
   of _get_net_connections().
 - add FIJISearchWidget to the dialog and call _add_driver_radiobutton_list
   from its callback after filtering the driver list

Related to vecs/fiji#60

(use_vars is default anyway thus drop it)

fixed invalid comparison and unnecessary print

Log it as an error but do not report it as such to certain callbacks thus
allowing to still save a replay configuration after an abort.

The dialog offers now:

* Substring search (searches for the entered string as substring)
* Globbing (converts glob to regex by FIJI::TextGlob)
* Conventional Perl Regexes

Otherwise, arguments to long options given with '=' are
not globbed.

Adress issue vecs/fiji#62

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