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This gets the main script working, and the pom compiling things.
To get it working right, two options were added for outputting normal &
error outputs to files instead of the standard streams (System.out &
System.err)
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Adds support for arranging files into groups. This may not be the final
way this feature looks, but it works.
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This is for when you have a large number of files and exceed the max
number of arguments, as well as preperation for a future feature
allowing the affixes to be grouped by source (essentially, grouped by
originating mod)
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