This avoid to put the pom.xml file into the source directory. Normally the pom file is in a parent (/parent) folder and it is not mixed with the java source code.
An other thing is: this will make import of the project more easy from a IDE.
The side effect is that the target folder where maven build artifacts will move from the <flatbuffers>/java/target to <flatbuffers>/target therefore the gitignore file has been updated in consequences.
Romain Gilles