Java JNI libraries have already been compiled for 32 and 64 bit versions of 
Windows and Linux. However, if you want to build your own, see below.


FOR LINUX
=======================
Compile the Java source:

javac -source 1.4 -target 1.4 -bootclasspath jdk1.4_rt.jar:jdk1.4_tools.jar -extdirs "" edu/ucsd/cs/riffa/*.java
javah -jni -o jriffa.h edu.ucsd.cs.riffa.Fpga

The -source -target -bootclasspath -extdirs flags on the javac command are used
to provide JDK 1.4 backwards compatibility. They are not needed if you are 
compiling this for your own JDK version.

Compile the JNI wrapper source:

gcc -I/usr/lib/jvm/java-7-oracle/include -I/usr/lib/jvm/java-7-oracle/include/linux -fpic -c -ojriffa.o jriffa.c
gcc -shared -o libjriffa.so jriffa.o -lriffa

Note that the riffa C/C++ library must already be installed on the system. The 
include directories may be different on your system. You'll need to adjust 
accordingly. You will also want to determine what value your Java JVM provides 
for system property os.arch. This will determine i386 (32 bit) or amd64 (64 bit) 
for the path below.

Create the riffa.jar:

cp libjriffa.so native/[i386|amd64]/Linux

jar cvf riffa.jar edu/ucsd/cs/riffa/*.class native/i386/Linux/* native/amd64/Linux/*

You can include other libraries in the jar. These are just the Linux ones.


FOR WINDOWS
=======================
Compile the Java source:

javac -source 1.4 -target 1.4 -bootclasspath jdk1.4_rt.jar;jdk1.4_tools.jar -extdirs "" edu\ucsd\cs\riffa\*.java
javah -jni -o jriffa.h edu.ucsd.cs.riffa.Fpga

The -source -target -bootclasspath -extdirs flags on the javac command are used
to provide JDK 1.4 backwards compatibility. They are not needed if you are 
compiling this for your own JDK version.

Compile the JNI wrapper source:

gcc -I"C:\Program Files\Java\jdk1.7.0_21\include" -I"C:\Program Files\Java\jdk1.7.0_21\include\win32" -I<path to dir containing riffa.h> -fpic -c -ojriffa.o jriffa.c
gcc -shared -o libjriffa.dll jriffa.o -L<path to dir containing riffa.dll or riffa.lib> -lriffa

Use the mingw gcc compiler or Microsoft's Visual Studio. Do not use the cygwin 
gcc compiler as it will add a dependency for the cygwin.dll.

Note that the riffa C/C++ library must already be installed on the system. The 
include directories may be different on your system. You'll need to adjust 
accordingly. You will also want to determine what value your Java JVM provides 
for system property os.arch. This will determine x86 (32 bit) or amd64 (64 bit)
for the path below.

Create the riffa.jar:

copy libjriffa.dll native\[x86|amd64]\Windows

jar cvf riffa.jar edu\ucsd\cs\riffa\*.class native\x86\Windows\* native\amd64\Windows\*

You can include other libraries in the jar. These are just the Windows ones.