On Worklight 6.2, if I create a directory anywhere under iphone/native called LibInclude, Worklight hides that directory and any contents in the Project Explorer view. It will show up in the Pending Changes view if you use Jazz SCM, but when you try to check in any files, it will give an error about not being able to find the file. If I create LibInclude anywhere NOT under iphone/native, it works normally.
This is an issue because Xtify uses a folder with this name for some files in it's SDK, and we can't check the files into SCM.
To recreate, create a WL project with an iPhone environment. Then in your OS browser, navigate to iphone/native and create a folder called LibInclude. Go back to eclipse and refresh from the Project Explorer view, and the folder you created will not be visible.
This works correctly in WL 6.1.
If there's any more info I can provide, please let me know.