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I've tuned the arm parameters a bit more, so they may well not run on the pi1 but should do better on pi2 + pi3.
Added them into artoolkit, flandmark, libfreenect and libdc1394 so they seem to build OK for arm too, and modified the pom.xml for flycapture so it will skip the cppbuild but produce a jar.
This means that:
mvn install -Pffmpeg -Djavacpp.platform=linux-armhf -Djavacpp.platform.compiler=arm-linux-gnueabihf-g++ -Dplatform=linux-armhf -Dplatform.compiler=arm-linux-gnueabihf-g++ -Dmaven.test.skip=true
Builds fine. So that should be I'll be able to add into Jenkins and get the produced jars automatically into Maven (either automatically on new commits, or just for tags).
(something seems up with openssl-1.0.2f - I think they've moved to version g, but I get something about needing to re run make depends with that and then build failures)