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The original fx-9860-derived "miniSDK" contains some strange design decisions. Some of these have been improved in libfxcg, mostly by moving header files around and renaming some functions. The full list of renamed functions is given in Category:Renamed Syscalls.
Many older programs will not compile successfully with the new libfxcg. It used to be the case that defining the symbol _FXCG_MINICOMPAT mapped old names to the new headers, but this has been removed.