My file structure on Windows:
\sites (*symlink to ..\sites)
When the PHPStorm root (where .idea folder is created) is set to "\core", then debugging just doesn't work at all for breakpoints set in files in \sites folder.
When the root is set to "\parent", then IDE complains about multiple declarations and has problems with completion, member resolution and inheritance analysis of classes.
So, it doesn't work well either way.