I think I understand what you have done here, but I may be wrong.
Never store files in the MATLAB toolbox directories. NEVER do that.
Having done that, you need to understand that those directories are cached. So changes made to those directories are not seen by MATLAB, at least not until you force MATLAB to update the toolbox cache, or until you restart MATLAB.
The path in question is (or should be) outside the installed MATLAB directories. Originally that was a local path where SVN checked out our scripts and classes.
Restarting Matlab doesn't clear it. Neither does installation of updates and new versions. It's hidden somewhere.