Hi guys,
Is there a good tool in java to manage meshes?
Such cleaning, multiple reference removal, merging close vertices, make indices and so on?
Basically Blender without the UI,… and in Java. 
I’d love there to be such a library, too!
But a quick solution would be to run Blender in headless mode and pass it Python scripts to execute, which contain the mesh modifiers.
Then export as an easy to import format, such as Wavefront OBJ.
With this you get the whole Blender awesomeness and power with an easy to use Python interface. Just integrating via an externalized mesh format may not be the best solution if you plan to modify a mesh thousands of times per frame.