Gradle cleanup

[pupnewfster]

Changes proposed in this pull request:

• Cleaned up deprecated Gradle calls
• Rewrote gradle calls slightly to remove the majority of IntelliJ warnings on the build.gradle file. The one change I am not too sure about is moving the maven publication to a closure and setting the project for it
• Copy the modified mods.toml file to the intellij build folder in addition to the gradle build folder. This only somewhat helps as the intellij runconfigs have the wrong paths for MOD_CLASSES by default, but now if they get manually fixed it can actually run now. (I didn't bother experimenting with manually specifying the values as I am fine with continuing to just use the gradlle intellij runconfigs
• Moved a lot of the all jar merge logic into a separate file and add support for merging tags that are added by multiple modules. In theory I think this fixes all the remaining merge issues the all jar had.