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The source code files have all been modified such it can conditionally build for either Gameboy Color or for Analogue Pocket.
The secondary step of needing to go into the lib folder and compiling that folder is no longer required. This is now done automatically, once for Gameboy Color, and again for the Analogue Pocket build, by the main compilation batch file.
The key thing now, is that any and all additional code that reads from and writes to STAT_REG or LCDC_REG needs conditional code.