So I have a winform solution, deployed via clickonce.
Eveything worked fine until i added a WCF project. (see error in parsing the manifest file at end of post)
Now I notice that MSBuild compiles the service into a _PublishedWebsites dir.
I don't know what the need for this is, but I am suspecting this is the cause of the problem. This wcf project references some other projects within the solution.
I am actually hosting the wcf service within the application so I don't really need MSBuild to do all this for me.
Any ideas?
=====================================================================================
 PLATFORM VERSION INFO
 Windows    : 5.1.2600.131072 (Win32NT)
 Common Language Runtime  : 2.0.50727.3603
 System.Deployment.dll   : 2.0.50727.3053 (netfxsp.050727-3000)
 mscorwks.dll    : 2.0.50727.3603 (GDR.050727-3600)
 dfdll.dll    : 2.0.50727.3053 (netfxsp.050727-3000)
 dfshim.dll    : 2.0.50727.3053 (netfxsp.050727-3000)
SOURCES
 Deployment url   : file:///C:/applications/abc/dev/abc.Application.application
IDENTITIES
 Deployment Identity  : Flow Management System.app, Version=1.4.0.0, Culture=neutral, PublicKeyToken=8453086392175e0f, processorArchitecture=msil
APPLICATION SUMMARY
 * Installable application.
 * Trust url parameter is set.
ERROR SUMMARY
 Below is a summary of the errors, details of these errors are listed later in the log.
 * Activation of C:\applications\abc\dev\abc.Application.application resulted in exception. Following failure messages were detected:
  + Exception reading manifest from file:///C:/applications/abc/dev/1.4.0.0/abc.Application.exe.manifest: the manifest may not be valid or the file could not be opened.
  + Parsing and DOM creation of the manifest resulted in error. Following parsing errors were noticed: 
   -HRESULT:  0x80070c81
    Start line:  0
    Start column:  0
    Host file:
  + Exception from HRESULT: 0x80070C81
COMPONENT STORE TRANSACTION FAILURE SUMMARY
 No transaction error was detected.
WARNINGS
 There were no warnings during this operation.
OPERATION PROGRESS STATUS
 * [12/03/2010 6:33:53 PM] : Activation of C:\applications\abc\dev\abc.Application.application has started.
 * [12/03/2010 6:33:53 PM] : Processing of deployment manifest has successfully completed.
 * [12/03/2010 6:33:53 PM] : Installation of the application has started.
ERROR DETAILS
 Following errors were detected during this operation.
 * [12/03/2010 6:33:53 PM] System.Deployment.Application.InvalidDeploymentException (ManifestParse)
  - Exception reading manifest from file:///C:/applications/abc/dev/1.4.0.0/abc.Application.exe.manifest: the manifest may not be valid or the file could not be opened.
  - Source: System.Deployment
  - Stack trace:
   at System.Deployment.Application.ManifestReader.FromDocument(String localPath, ManifestType manifestType, Uri sourceUri)
   at System.Deployment.Application.DownloadManager.DownloadManifest(Uri& sourceUri, String targetPath, IDownloadNotification notification, DownloadOptions options, ManifestType manifestType, ServerInformation& serverInformation)
   at System.Deployment.Application.DownloadManager.DownloadApplicationManifest(AssemblyManifest deploymentManifest, String targetDir, Uri deploymentUri, IDownloadNotification notification, DownloadOptions options, Uri& appSourceUri, String& appManifestPath)
   at System.Deployment.Application.ApplicationActivator.DownloadApplication(SubscriptionState subState, ActivationDescription actDesc, Int64 transactionId, TempDirectory& downloadTemp)
   at System.Deployment.Application.ApplicationActivator.InstallApplication(SubscriptionState& subState, ActivationDescription actDesc)
   at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
   at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)
  --- Inner Exception ---
  System.Deployment.Application.InvalidDeploymentException (ManifestParse)
  - Parsing and DOM creation of the manifest resulted in error. Following parsing errors were noticed: 
   -HRESULT:  0x80070c81
    Start line:  0
    Start column:  0
    Host file:
  - Source: System.Deployment
  - Stack trace:
   at System.Deployment.Application.Manifest.AssemblyManifest.LoadCMSFromStream(Stream stream)
   at System.Deployment.Application.Manifest.AssemblyManifest..ctor(FileStream fileStream)
   at System.Deployment.Application.ManifestReader.FromDocument(String localPath, ManifestType manifestType, Uri sourceUri)
  --- Inner Exception ---
  System.Runtime.InteropServices.COMException
  - Exception from HRESULT: 0x80070C81
  - Source: System.Deployment
  - Stack trace:
   at System.Deployment.Internal.Isolation.IsolationInterop.CreateCMSFromXml(Byte[] buffer, UInt32 bufferSize, IManifestParseErrorCallback Callback, Guid& riid)
   at System.Deployment.Application.Manifest.AssemblyManifest.LoadCMSFromStream(Stream stream)
COMPONENT STORE TRANSACTION DETAILS
 No transaction information is available.