Clean code and structure

.idea/.name

settings.gradle

src/main/java/fr/irit/smac/amas/Cluster.java

src/main/java/fr/irit/smac/amas/MASSettings.java

src/main/java/fr/irit/smac/amas/SimilarityScoreMethod.java

...a/fr/irit/smac/amas/controller/ClusterAMASController.java

...rit/smac/amas/controller/command/NewDataPointCommand.java

src/main/java/fr/irit/smac/clumate/CluMATE.java

src/main/java/fr/irit/smac/clumate/amas/AMASOption.java

src/main/java/fr/irit/smac/clumate/amas/ClusterAMAS.java

src/main/java/fr/irit/smac/clumate/amas/ClusterAgent.java

...in/java/fr/irit/smac/clumate/amas/ClusterEnvironment.java

src/main/java/fr/irit/smac/clumate/amas/MASSettings.java

.../irit/smac/clumate/amas/controller/CluMATEController.java

...fr/irit/smac/clumate/amas/controller/command/Command.java

.../clumate/amas/controller/command/NewDataPointCommand.java

...smac/clumate/amas/controller/command/ShutdownCommand.java

...it/smac/clumate/amas/controller/command/SolveCommand.java

...ava/fr/irit/smac/clumate/amas/controller/query/Query.java

...va/fr/irit/smac/clumate/amas/controller/query/Result.java