Treat projects in subfolders correctly in `NewFileWizard`

Normally a project is located in the root of the workspace, which would
lead to a physical location like '/workspace/project/file'. But it is
totally valid to have a file in a physical location like
'/worskpace/subfolder/project/file'. In this case the wizard did not
work correctly.

Fixes #1002185
I think this won't work for mapped resources. I belive the best way is to always use resources and workspace-relative operations. I see no reason to use the underlying file-system, since the wizard will probably get workspace-relative paths and `IFile` in the first place.