We've updated the Orchard Hungary sites to 1.6 a while ago and we're trying deploy it now using Visual Studio 2012. The process fails due to one specific file, which is \Media\web.config:
Could not open Source file: Could not find a part of the path 'C:\DEV\Orchard HUN\src\Orchard.Web\Media\web.config;Media\web.config'.
Since changeset #6437, this file is included in the Orchard.Web.csproj as "Content", instead of "None".
Resetting it to "None" solves the issue.
Related issue: http://orchard.codeplex.com/workitem/19264