Deprecate java.generate_native_header() in favor of java.generate_native_headers()

After implementing a much more extensive Java native module than what
currently exists in the tests, I found shortcomings.

1. You need to be able to pass multiple Java files.
2. Meson needs more information to better track the generated native
   headers.
3. Meson wasn't tracking the header files generated from inner classes.

This new function should fix all the issues the old function had with
room to grow should more functionality need to be added. What I
implemented here in this new function is essentially what I have done in
the Heterogeneous-Memory Storage Engine's Java bindings.

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