fix bug in sidecompoundscan app ignoring the dp option
fix bug in createmetanetwork app related to id merging

tag 2.0.1

This reverts commit 5ec45018.

release 2.0.0

* a lot of overly specific exports
* mainly focused on compoundgraph and bipartite
* lacks of flexibility regarding attributes export
* a lot of duplicated code in apps
* gml as default and lacks of node export in app not adapted for workflow

Add:

* an utility class for apps exporting graphs
* parametrizable export
* harmonization and support for all graph types
* node table export in apps

Clean apps

See merge request !37

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

Biblio app

See merge request !35

* Add getDois method in AbstractMet4Application
* Generate references in doc from dois by querying the crossref api
* add citation tags into galaxy xml wrapper

Creation of multi-network

See merge request !32

fix Protein/gene names in FBC parser