I'm getting warnings and notices for my theme which do not correspond to the files in my theme. Even after re-installing the plugin.
Does the plugin cache the theme files? I'm getting recommended changes for code, like removing bloginfo('url'), which does not exist in any of my theme's files, and hasn't for some time. And warnings to include things like comment_form() and get_search_form() which I do, sometimes in multiple files, but for some reason this plugin cannot seem to find them in the php files.