There is a library called jnigen [1], mainly used by the libGDX framework [2]. But I don't see it used in many other projects though. Personally I use it to maintain a set of Lua C API bindings for some platforms [3] and it works sort of OK once you manage to somehow set up a workflow for building and testing the binaries.

> It works but it is a pain if anything ever changes or a new platform needs to be brought up. Checking in binaries always feels icky but is necessary if not all targets can be built on a single machine.

It is definitely a pain when you cannot test all changes on a single local machine. But I would argue that it is true whenever multiple platforms (or maybe even multiple glibc versions) are involved, regardless of what languages/libraries/tools you use.

[1] https://libgdx.com/wiki/utils/jnigen [2] https://github.com/libgdx/libgdx [3] https://github.com/gudzpoz/luajava