Release Notes for Darwin

NOTE: if you are upgrading from 2.1 (any version) to 2.2, you will have to deal with the fact
that colonies (of organisms) now belong to populations.  And, in particular, an environment
is no longer part of a population, it is now part of a colony.  There are some other relatively
minor name changes to deal with too.

   * Version 2.2.05
      * Changed name of Darwinian type family to Taxon;
      * Enabled the use of include to logically separate different parts of the configuration;
      * Enabled support for adding beans as map members where bean itself is the key; 
      * (requires 1.0.11 of beanpot).

   * Version 2.2.04
      * Fixed a problem in evolution utilities such that some exceptions were being ignored.
      * Fixed problem with traveling salesman whereby a poisson distribution fitness checkvcould be invalid because of scaling issues (it now resets the scale and starts the wholevgeneration over).
      * There are more checked exceptions now and more cases of throwing existing exceptions, eg. Function_Exception, Fitness_Exception, Value_Exception.

   * Version 2.2.03
      * Refactored Evolution classes to fix some issues with termination.
      * Evolution class now implements preConfigure and postConfigure methods.

   * Version 2.2.02
      * Darwin now supports the setting of an explicit class loader (by using version 1.0.10 of beanpot);
      * Evolvers can now set a clock watcher which will be triggered when each new tick occurs;
      * Fecundity getFecundity signature changed to take a Colony;
      * Refactored many of the UI classes so that they are now properties of the applet;
      * Renamed
         * Fitness_Standard as Fitness_Hamiltonian
         * Mating_Standard as Mating_Haldanian;
         * MateChoice_Experience as MateChoice_Wrightian.

   * Version 2.2.01 (equivalent to 2.1.14)
      * Traveling Salesman solution now works significantly better than before;
      * Fixed the Population_Splitting situation such that the total population before and after splitting is appropximately the same;
      * Changed name of Population_Splitting to Population_Managed;
      * Also added a property to cap the number of colonies in a Population_Managed;
      * Renamed Phenome_Standard to Phenome_Gouldian.

   * Version 2.1.13
      * Significant refactoring such that Colonies now belong to Populations and Environments belong to Colonies
      * Refactoring of ExPhen, Expresser, Population classes to help improve TS application;
      * Added Best family of classes.

   * Version 2.1.12
      * Use 1.0.1 version of ToString so that we can evaluate Calendar objects as Strings using own method.

   * Version 2.1.11
      * Refactoring of Mating/Choosiness classes (in particular, added Lek).
      * Significant performance increase.

   * Version 2.1.10
      * Refactoring of Evolution classes

   * Version 2.1.9
      * Audit classes split off into separate project: toString0

   * Version 2.1.8
      * Reworked Audit classes.

   * Version 2.1.7
      * Refactored census classes.

   * Version 2.1.6
      * OutOfTheBox application now works.

   * Version 2.1.5
      * Minor refactoring changes.

   * Version 2.1.4
      * Minor refactoring changes.  Allele classes are better designed now.  Some class names and constructor arg sequences have changed.

   * Version 2.1.3
      * Add the ability to specify beans as a keyed member of another bean (in the configuration file) -- this replaces the way that it had to be done previously by setting all members at once in a map.

   * Version 2.1.2
      * Add the ability to specify beans as a member of another bean (in the configuration file) -- this replaces the way that it had to be done previously by setting all members at once in a list.

   * Version 2.1.1
      * The correspondence between Visualizables and Visualizers and VisualizationModels is now determined by the configuration file.
         * Requires BeanPot 1.0.7.

   * Version 2.1.0
      * Configuration file has changed to take advantage of BeanPot 1.0.6: [IMPORTANT: if your configuration file specified an applet or a singleton bean, the file must be edited in order to use this version.  See the configuration document for more details].
         * concept of external beans has been generalized (formerly only dealt with applets);
         * bean container now has an identifier which can be used to name the application/applet;
         * no longer uses properties file for any of the configuration;
         * version identifier now derives from the framework source itself;
      * Added three new applet parameters:
         * beans (the name of the bean configuration file); and
      * showBeans (a boolean - if true then the bean configuration is output to console).
      * enableSlider (was formerly in the properties file).

   * Version 2.0.5
      * Restored reference to mutator for peppered moth in config file;

   * Version 2.0.4
      * Now choosiness is enabled;
      * Still working on slider issues;

   * Version 2.0.3
      * Bug fix for applet running over internet
         * Now check that it's OK to stop threads;
         * ... if not, then we don't enable the generation rate slider;
         * Added version string on options panel;

   * Version 2.0.2
      * Mostly cosmetic changes (fixing a few PMD violations)
         * Replaced lost class (Registry_None)

   * Version 2.0.1
      * New Darwin 2
         * Please see new.txt for some background to this version.