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Major refactor #2

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Major refactor #2

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ammendes
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Major refactor of the entire codebase. We now have two accessory classes: Utils.Java and CLUtils.Java, which encapsulate all methods used. Utils.Java handles all non-OpenCL methods, and CLUtils.Java handles all OpenCL-based methods.

- Tested new kernel, its OK
different SReD modes now have a parent class.
 All methods are transported to accessory classes.
Two accessory classes were made: CLUtils contains all methods using OpenCL, Utils contains the rest.
Need to test block repetition 3D, and all global repetition kernels, but block repetition 2D is tested.

This refactor makes the code more readable, more organized, and should allow easier CI.
Fixed incongruences with newer methods in older classes.

Classes other than Block repetition and global repetition need improvement.
Added support for 2d block repetition using timeframes
corrected bug where spurious values would be written in borders in kernels
Fixed some bugs. Added unit tests.
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