Add support for remapping jar mods with multiple --in-jar

You can now pass multiple filenames to --in-jar, and the files
in the subsequent jars will overwrite those in the previous. This
allows remapping "jar mods", which are distributed as an archive of
a subset of files against a reference jar. For example, Forge
overwrites base classes in Minecraft. Example usage:

java -jar target/SpecialSource-1.3-SNAPSHOT-shaded.jar --in-jar http://assets.minecraft.net/1_4_7/minecraft_server.jar --in-jar http://files.minecraftforge.net/minecraftforge/minecraftforge-universal-1.4.7-6.6.2.534.zip --out-jar /tmp/n/test.jar --srg-in https://raw.github.com/MinecraftForge/FML/master/conf/