Refactoring in commit a2514f15 (Simplify cmNinjaTargetGenerator using
cmGeneratorTarget, 2012-03-13) accidentally removed mapping of .def file
paths through ConvertToNinjaPath (via GetSourceFilePath).  Take the
ModuleDefinitionFile value from cmGeneratorTarget and map it correctly
through ConvertToNinjaPath.

In addition to generating cleaner paths in the ninja build files this
correctly links up references to a generated .def file with the custom
command output that produces it.