Normalizing the project

* Removing some obsolete stuff and history leftovers
* Removing some errors & warnings
* First steps towards changes yet to come
Renaming project name to "pikater-core"

This allows better distinction in eclipse and any eventual git submodules.
Renaming "libraries" folder to "lib"

According to standards.
Normalizing test related code

* Created the "test" folder and added it as a source folder.
* Moved all ".java" files from "core/inputsKlara/" to the new test folder.
* Moved the "tests" package to the new test folder and organized the files to be much better structured and usable.

TODO:
* Rewrite the tests into proper JUnit tests. Don't run as "java application"...
Fixing code to reflect recent changes

* Agent_GUIKlara doesn't load any "input.xml" file now. Instead, it uses test experiments directly through the "Beans.xml" file. The "--run" option has been preserved to load arbitrary XML files containing serialized "ComputationDescription" objects.
* Removing some obsolete stuff.