This was a real adventure since I didn’t know anything about SCons, and
I can’t say that I’m fond of scons after it, but it does seem to work.
There were two obstacles.

First, the ConfigureJNI module doesn’t successfully configure the JNI on
my system because it was expecting to find `JAVA_HOME` in .., so I added
a little code to notice if it’s failing to find a place where `jni.h`
exists.  (And on my system I did `export
JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64` before running it, but your
pathnames will vary.)  There was a hardcoded pathname in SConscript,
presumably as an interim debugging measure, which I removed.  A
reasonable default to try on Debian-derived systems such as Ubuntu and
LinuxMint might be `/usr/lib/jvm/default-java`, but I didn’t implement
that.

Second, in SConscript, the JNI include directories were being stuck into
a `javaenv` SCons environment object, which was used to build the Java
classes providing the Java interfaces to Hammer, but not the C files
containing the native methods themselves.  Consequently the compiler
couldn’t find the JDK JNI headers when it tried to compile the C code
into a shared library.  It might make sense to use `javaenv` to compile
that shared library, but in case it doesn’t, I cloned the default
environment with an extra include directory.

I hope this is soon enough to be helpful!