I'm using the statusbar plugin on iOS to keep the status bar from overlaying the webview.
<preference name="StatusBarOverlaysWebView" value="false" />
I put this preference in plugins/ios.json's munge section and in config.xml.
If I remove the platforms/ directory and then add the ios platform back in, the statusbar plugin does not load. The status bar is now transparent instead of my preference.
The only way to get it reconfigured properly seems to be to remove and re-add the plugin but even this fix does not seem to be completely reliable.