Clean apps

The goal was to check the met4j-toolbox apps, especially :

* names of the apps
* documentation
* names of the parameters to be consistent between apps

We applied these rules :

* Starting the name of an app by Sbml is useless since almost all apps take SBML as input.
* The name must be concise and meaningful
* Sbml in the name of an app must be written in camel case, not SBML
* The short description must be as concise as possible
* The parameter for the main input must be -i
* The parameter for the main output must be -o
* System.err must only be used for errors not logs
* When two formats of output are possible (ex: GML or TSV), indicate Txt

To make consistent the behaviour of the apps, some utils methods will be created:

* readSbml with options to select the packages uses
* writeSbml
* getMetabolitesFromFile especially used for side compound import