When using pom-imagej based dependencies and imglib2 and other libraries make sure you update the local version of scijava-common which supports parallel building without the concurrentmodificationexception

The tipl-libraries submodule folder will be empty unless you perform a

git clone --recursive

if you forget this step you can still fix it by performing

git submodule update --init

After making many updates it is often easier to do a batch commit

commitMessage="Test Message"
git add pom.xml
git add *.iml
for cDir in */; do 
    cd $cDir; 
    git add pom.xml; 
    git add --all src; 
    git add *.iml; 
    cd ..; 
done
cd ccgeom/
git commit -m "$commitMessage"
cd ../volviewer
git commit -m "$commitMessage"
cd ../VIB-lib/
git commit -m "$commitMessage"
cd ..
git commit -m "$commitMessage"

To push all

cd ccgeom/
git push
cd ../volviewer
git push
cd ../VIB-lib/
git push
cd ..
git push

• The project is meant to be built in a Java first then Scala manner with the exception of a few files. Primarily ScalaPlugins.java which is used for loading the Plugins written in Scala into the SezPoz-based TIPLPluginManager. A simple space entered into this file and save will cause it to recompile after the scala code has been compiled resolving all errors.
• The IDEA compiler can cause issues, using the SBT incrementally type works better

The TIPL code itself is separated from Spark but involves the spark code in a number of key areas.

• SGEJob sets up the path and includes reference to the jumbo jar file in the spark/lib folder, many tasks unrelated to Spark will not work if this is missing (to prevent library duplication)