FIJISettingsViewer and FIJITestsViewer are widgets and can refere to
their root windows via $self->MainWindow thus there is no need to
store them additionally.

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

Previously, the user was asked to supply a valid FIJI config repeatedly if
none was provided. Even canceling the dialog would not end the
application.

With this patch the user is asked repeatedly only if it is not valid (throwing
errors). If the user cancels loading the config file, EE GUI aborts completely.

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

 - 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

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.

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.

Since the appender is defined in logger.conf and thus loaded by all
applications we need to remove it at load time from all applications
but the CLI EE tool.

I.e. fix the chaos that has been growing for a while and the bugs
introduced in the patch
"fiji_ee_gui: allow to abort test runs even during long transfers"

 - make all of them a function
 - use the same parameter and return scheme for said function
 - unify indentation, wording and parameter names
 - document verbosity parameter

Use this to set the available UART ports and default timer values.
The latter gets rid of FIJI::DEFAULT_TIMER_VALUE by replacing it with
FIJI::Settings::default_timer_value().

However, it requires some non-trivial changes, namely the refactoring
of FIJI::Tests. While at it, we got almost rid of the 'ext' field in
Tests. It is lessened to 'TESTPATMAP' containing info to verify tests.

The refactoring also allows for unification of opening of tests files
in the EE GUI. To that end this patch adds _read_tests_file() that
handles creation of the Tests instance and handle user interaction if
need be.

 - add a new pattern to the logger.conf file (and a fallback
   one hardcoded to FIJITestsViewer)
 - parse the config file within FIJITestsViewer and change the layout
   pattern of the QueueAppender accordingly
 - make sure the download worker uses the same logger configuration
   as the main thread by re-applying the same changes in the worker thread
 - also, add indentation to ordinary multi-line log messages

They are generated by DialogBoxUL automatically.

 - Change FIJIModalDialog to handle markup text with URLs.
 - Add a unified about text in a file.
 - Create a central show_about() and use that in Setup and EE.

TODO: docs/