[Amibe] Add Mesh.checkAdjacency and Mesh.clearAdjacency

They are only debugging methods
[Amibe] make Mesh.rebuildVertexLinks and glueSymHE public
[Amibe] Add comment to AHE.getNeighbourIteratorAbstractHalfEdge
[OccJava] Update .gitignore with some generated files
[Amibe] Add Skeleton.getByGroups
[Amibe] TriangleKdTree.getNearTriangles