I checked the source code of CMake (both 2.8.12.2 and 3.0.0); CMake seems to add the current source directory of all paths that don't start with '/' on windowless systems.
Only exception is the expression of the generator. If the path starts with "$ <", then it skips the path prefix and not the prefix after evaluating the generator expression. therefore
include_directories(AFTER SYSTEM "$<1:=>/usr/include")
generates
-isystem =/usr/include/
This seems to work, at least for CMake 3.0.0. Of course, you must set CMAKE_SYSROOT for gcc for the prefix with the correct path.
set(CMAKE_SYSROOT /usr/arm-linux-gnueabi)
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