[Build] Unify build output and classpath configurations

[HannesWell]

Avoid using PDE's 'requiredPlugins'-container together with M2E's 'MAVEN2_CLASSPATH_CONTAINER'-container. When using both at the same time, one only ensures that Maven and PDE dependencies combined work, which is never a real use-case.

Also fix multiple build-configuration related warnings.

[NiklasRentzCAU]

I am not quite sure about some of these changes, let me elaborate the thought behind this current setup:
KLighD is historically developed in Eclipse and provides Eclipse Plug-Ins, which is why most build on Plug-In dependencies in the Eclipse configuration. However, KLighD is also available as an Eclipse-less standalone/language server variant, which does not use any of the Plug-In dependencies, but Maven dependencies via their pom.xml. The dependencies are not entirely duplicated but mostly put into poms for the setup/ls containing all further downstream dependencies.

Now because of this setup, most projects are also Maven projects so that Eclipse handles them correctly. Eclipse then does some automatic changes to the code, including for example the change of using target/classes as the default output instead of bin which I would therefore like to keep that way.
The PDE/M2E containers seem like an error to me as well and should only have one. piccolo.freehep should probably only have the PDE container, while the setup and standalone should only have the Maven container; they are only ever executed as plain Java applications without PDE.