Attempt to cleanup the pom.xml.

Small entry in .gitignore to skip a Maven specific file.

Added a .gitattributes file to make sure line endings are constant cross
developers and platforms.

Divided app specific files into separate folders.

Some plugin updates:
* commons-codec -> 1.7
* jcommander -> 1.30
* junit -> 4.11
* launch4j-maven-plugin -> 1.5.2
* maven-compiler-plugin -> 3.0
* maven-jar-plugin -> 2.4
* maven-shade-plugin -> 2.0
* osxapp-maven-bundle -> 1.2-SNAPSHOT
* snakeyaml -> 1.11