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Update:
It seems the problem is not MVC. It seems to be with a new website created from visual studio 2010 (File > New Project > EPiServer Web Site). When I try to install Commerce on a website created in VS (Both MVC and Not MVC) I get this error in the installation process.
When I install commerce on a site created by EPiServer Deployment Center it seems to work fine. What is the difference between these site types? How can I fix this?
When I try to install Commerce R3 version 7.0.243.o on an existing CMS website (7.0.586) I get an exception saying "Error - Unable to get package metadata."
Details
Import Page provider Entry page
Setup default Association Type
Enable en-US language
Create roles for default admin
Copied ecf_CreateCMSRoles.sql
Installing packages
Installing packages
Installing package: EPiServer.Business.Commerce.AddOns.Manager.1.0.7.nupkg
Get-ChildItem : Cannot find path 'C:\Windows\AppData\Modules\7bd4eb37aa3e4b2382
044ed06a06e234' because it does not exist.
At C:\Program Files (x86)\EPiServer\Framework\7.0.859.1\Install\System Scripts\
Install Module Package.ps1:68 char:19
+ $itemsToRename = Get-ChildItem $folderToScan
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ CategoryInfo : ObjectNotFound: (C:\Windows\AppD...2044ed06a06e23
4:String) [Get-ChildItem], ItemNotFoundException
+ FullyQualifiedErrorId : PathNotFound,Microsoft.PowerShell.Commands.GetChi
ldItemCommand
An error has occured and the transaction will be rolled back
Failed to rollback copying of files from C:\Program Files (x86)\EPiServer\CMS\7.0.586.1\Install\Modules\EPiServer Commerce 7.0.243.0\Application to D:\TFS\***Commerce\Trunk\Source\***.com\***.com
Could not find file 'module.config'.
Rolledback