various tweaks & fixes

Mostly for
https://github.com/libgdx/libgdx/issues/2359
https://github.com/libgdx/libgdx/issues/2524
https://github.com/libgdx/libgdx/issues/2441
https://github.com/libgdx/libgdx/issues/2436

JDK collection behavior uses `.equals` comparison, except for `Identity*` classes.