I’ve got a SharePoint solution containing a standard SharePoint solution project and a SharePoint App project.  While trying to use CKS Dev to deploy mapped files for the standard SharePoint solution using context menu command Quick Deploy (CKSDev) > Copy to SharePoint Root I got the following error:

Could not load file or assembly ‘AssemblyName.dll’ or one of its dependencies.  The system cannot find the file specified.

Apparently CKS dev looks at all your SharePoint projects and attempts to load up the DLLs, even if your projects is a SharePoint App.  Unfortunately, SharePoint App projects do not compile into a DLL (because that would defeat the purpose).  CKS will probably fix this issue eventually, but if you encounter the error you can “trick” CKS dev into working by copying a DLL into your SharePoint App’s bin\debug\ folder and renaming the DLL to match the name of your project.  CKS dev will then work as expected.