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it is not necessary that JNI based implementations are better only because they are written in C
Agreed. My point is that in this case, the complete (and only) HDF5 reference implementation is written in C, so the Java libraries which simply interface with that are indeed likely to work much better, at least on supported platforms.
very limited number of platforms for which a JVM with java.nio exists
java.nio not available on the JVM on some platforms? I would expect it is there for Windows, macOS, Linux x86/x64, Linux ARM/ppc, Linux s390x (what is that?), Solaris, Solaris SPARC, AIX, z/OS, IBM i. That does not strike me as particularly limited?
de.mdc-berlin.preibischlabfor all your stuff?
SPIM_Registrationfork, even though the groupId is changed, would still make a JAR with the same name, and thus be overridden when you replace
SPIM_Registrationon your update site. (For some definition of "nice"—alternately it might make more sense to change the package prefix and artifactId so that both can coexist without conflict.)