Update,
It appears that the new file structure doesn't contain an include file/folder and importing
it from my previous project doesn't seem to work (meaning fails to recognize the MK64F12.h).
If instead I import to the CMSIS file/folder, then some of the defines are seen.
Curiosly enough, looking at the previous project, SDK 3.0, MK64F12.h appears in two areas, inside
the CMSIS and in the startup file/folder. Another observation is that the two MK64F12.h are different
and have different builds.
Yet another interesting issue is that the way I addressed the registers under SDK 3.0 is now not
recognized by 3.1.0? Example 3.0: UART0_PRC15 = some HEX value
Example 3.1: UART0->PRC[15] = some HEX value