Restructure ModelPolisher.

[codekaust]

As code related to docker needs to be added to ModelPolisher, the following issue was noticed. Currently, the src folder directly contains java packages, like edu/ucsd/sbrg/ followed by code packages, which is not ideal. Need to make the following changes:

• Move packages from current src/ to src/main/java/
• Move resources from resources/ to src/main/resources/
• Move test codes currently in test/ to src/test/java/
• Add folder src/main/docker/ to add code related to containeristion using docker
• Make changes accordingly to build process

[draeger]

As discussed with @matthiaskoenig, we don't need to create the folder /src/main/docker/, but restructuring the other locations still makes sense. In this way, the project will become more standardized and tidier.