Class name refactoring affecting entire core platform code Follow

Today I renamed an inner PRIVATE class in a java class, and it refactored the classname in the entire platform code base (non-custom) and custom code and I spent hours trying to clean it up then finally gave up.

As powerful as IJ is, why doesn't it have the capability of distinguishing between different classes named alike in different packages ?? It did a horrible string- replace !! And the corny thing is, git did not even show any differences after that, ant sure as hell did, with different results on every run.