adding changes
adding new generic scripts
Added Generic Analysis scripts/programs
created and updated analysis tools, parallelism
Updates to the parallel branch, using a thread pool to create parallel
tasks.  Seems faster, but maybe uses too much memory for bigger
networks.
Removed libs, moving towards maven
Adding missing/moved files
fixed some problems with using EdgePair instead of the full EdgeEntry
Added mvn multi-module parent
Added commons-math as dependency
Updated runnable mains, made it easier to call analysis as a library
Changed tools to be more generalizable, user-friendly
fixed problems with benchmark tool
Separated RJava and base libraries, adopting jannotater plugin
Updated package for R code.  Adapted benchmarks to be executable from R,
        moved some things around
Merge /home/jfolson/Projects/DynamicJUNG
Reorganized the directory and migrated to gradle for build tools
No need for separate directories with the gradle plugin
Moved because gradle plugin does not require separate directories
Adding skeleton of the R package, removing auxiliary tools that I
haven't checked in a long time and forgot how they work.