Publish a ClickOnce deploy with Visual Studio and assemblies not referenced
When you build a ClickOnce deploy Visual Studio do not get assemblies not referenced in the project or any other dependent project. Basically the problem are assemblies located in other folders than the project folder.
But you can workaround this issue overriding two targets in your project, both targets are located in Microsoft.Common.Targets. The basic idea is generate a new target file that your project references.
The first target is _DeploymentComputeClickOnceManifestInfo, which is executed before the beginning of the publishing. Copy this target to a file called Customized.targets, and add your logic in order to include the assemblies that Visual Studio do not include.
For example if want to include all the assemblies located in the modules subfolder we need to add the following tasks:
<Target Name="_DeploymentComputeClickOnceManifestInfo"
Condition="'$(GenerateClickOnceManifests)'=='true'"
DependsOnTargets="_DeploymentGenerateTrustInfo">
<CreateItem Include="@(_ReferenceSerializationAssemblyPaths)"
Condition="'%(Extension)' == '.dll'">
<Output TaskParameter="Include" ItemName="_SGenDllsRelatedToCurrentDll0" />
</CreateItem>
A0A0A0 <CreateItem Include="@(_SGenDllsRelatedToCurrentDll0->'%(FullPath)')">
A0A0A0A0A0A0A0 <Output TaskParameter="Include" ItemName="_SGenDllsRelatedToCurrentDll" />
A0A0A0 </CreateItem>
A0A0A0 <CreateItem Include="@(ReferencePath)" AdditionalMetadata="IsPrimary=true" >
A0A0A0A0A0A0A0 <Output TaskParameter="Include" ItemName="_DeploymentReferencePaths"/>
A0A0A0 </CreateItem>
A0A0A0 <ResolveManifestFiles
EntryPoint="@(_DeploymentManifestEntryPoint)"
ExtraFiles="$(IntermediateOutputPath)$(TargetName).pdb;$(IntermediateOutputPath)
$(TargetName).xml;@(_ReferenceRelatedPaths)"
Files="@(ContentWithTargetPath);@(_DeploymentManifestIconFile);@(AppConfigWithTargetPath)"
ManagedAssemblies="@(_DeploymentReferencePaths);@(ReferenceDependencyPaths);
@(_SGenDllsRelatedToCurrentDll)"
NativeAssemblies="@(NativeReferenceFile);@(_DeploymentNativePrerequisite)"
PublishFiles="@(PublishFile)"
SatelliteAssemblies="@(IntermediateSatelliteAssembliesWithTargetPath);@(ReferenceSatellitePaths)"
TargetCulture="$(TargetCulture)">
A0A0A0 <Output TaskParameter="OutputAssemblies" ItemName="_DeploymentManifestDependencies"/>
A0A0A0 <Output TaskParameter="OutputFiles" ItemName="_DeploymentManifestFiles"/>
A0A0A0 </ResolveManifestFiles>
A0
A0A0A0 <!-- Generate all dependencies -->
A0A0A0 <CreateItem Include="$(OutputPath)Modules\**\*.dll">
A0A0A0A0A0A0A0 <Output TaskParameter="Include" ItemName="DeploymentManifestModules" />
A0A0A0 </CreateItem>
A0A0A0 <CreateItem Include="@(DeploymentManifestModules)"
AdditionalMetadata="TargetPath=Modules\%(RecursiveDir)
%(Filename)%(Extension);DependencyType=Install">
A0A0A0A0 <Output ItemName="_DeploymentManifestDependencies" TaskParameter="Include" />
A0A0A0A0A0A0A0 </CreateItem>
A0A0A0A0A0A0A0 <!-- Generate all remaining files -->
A0A0A0A0A0A0A0 <CreateItem Include="$(OutputPath)Modules\**\*.xaml">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="Include" ItemName="LocalDeploymentManifestFiles" />
A0A0A0A0A0A0A0 </CreateItem>
A0A0A0A0A0A0A0 <CreateItem Include="@(LocalDeploymentManifestFiles)"
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 AdditionalMetadata="TargetPath=Modules\%(RecursiveDir)%(Filename)%(Extension)">
A0A0A0A0A0A0A0A0A0A0A0 <Output ItemName="_DeploymentManifestFiles" TaskParameter="Include" />
A0A0A0A0A0A0A0 </CreateItem>
A0
A0A0A0A0A0A0A0 <CreateProperty Value="ClickOnce">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="Value" PropertyName="_DeploymentManifestType"/>
A0A0A0A0A0A0A0 </CreateProperty>
A0
A0A0A0A0A0A0A0 <FormatVersion Version="$(ApplicationVersion)" Revision="$(ApplicationRevision)">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="OutputVersion" PropertyName="_DeploymentManifestVersion"/>
A0A0A0A0A0A0A0 </FormatVersion>
A0A0A0A0A0A0A0 <FormatUrl InputUrl="$(_DeploymentUrl)">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="OutputUrl" PropertyName="_DeploymentFormattedDeploymentUrl"/>
A0A0A0A0A0A0A0 </FormatUrl>
A0A0A0A0A0A0A0 <FormatUrl InputUrl="$(SupportUrl)">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="OutputUrl" PropertyName="_DeploymentFormattedSupportUrl"/>
A0A0A0A0A0A0A0 </FormatUrl>
A0A0A0 </Target>
The lines added to the original target are in italic format.
The second target to override is _CopyFilesToPublishFolder, the change here is easy, simply add the metadata variable %(RecursiveDir) for each item list that you want to copy.
A0A0A0 <Target Name="_CopyFilesToPublishFolder">
A0A0A0A0A0A0A0 <FormatVersion Version="$(ApplicationVersion)" Revision="$(ApplicationRevision)"
FormatType="Path">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="OutputVersion"
PropertyName="_DeploymentApplicationVersionFragment"/>
A0A0A0A0A0A0A0 </FormatVersion>
A0A0A0A0A0A0A0 <CreateProperty Value="$(AssemblyName)_$(_DeploymentApplicationVersionFragment)">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="Value" PropertyName="_DeploymentApplicationFolderName" />
A0A0A0A0A0A0A0 </CreateProperty>
A0A0A0A0A0A0A0 <CreateProperty Value="$(PublishDir)$(_DeploymentApplicationFolderName)\">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="Value" PropertyName="_DeploymentApplicationDir" />
A0A0A0A0A0A0A0 </CreateProperty>
A0
A0A0A0A0A0A0A0 <!-- Copy files to publish folder -->
A0A0A0A0A0A0A0 <Copy
A0A0A0A0A0A0A0A0A0A0A0 SourceFiles=
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 "@(_ApplicationManifestFinal);
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(_DeploymentManifestEntryPoint);
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(_DeploymentManifestFiles);
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(ReferenceComWrappersToCopyLocal);
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(ResolvedIsolatedComModules);
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(_DeploymentLooseManifestFile)"
A0A0A0A0A0A0A0A0A0A0A0 DestinationFiles=
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 "@(_ApplicationManifestFinal->'$(_DeploymentApplicationDir)
%(TargetPath)%(RecursiveDir)');
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(_DeploymentManifestEntryPoint->'$(_DeploymentApplicationDir)
%(TargetPath)%(RecursiveDir)$(_DeploymentFileMappingExtension)');
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(_DeploymentManifestFiles->'$(_DeploymentApplicationDir)
%(TargetPath)%(RecursiveDir)$(_DeploymentFileMappingExtension)');
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(ReferenceComWrappersToCopyLocal->'$(_DeploymentApplicationDir)
%(RecursiveDir)%(FileName)%(Extension)$(_DeploymentFileMappingExtension)');
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(ResolvedIsolatedComModules->'$(_DeploymentApplicationDir)
%(RecursiveDir)%(FileName)%(Extension)$(_DeploymentFileMappingExtension)');
A0A0A0A0A0A0A0A0A0A0A0A0A0A0A0 @(_DeploymentLooseManifestFile->'$(_DeploymentApplicationDir)
%(RecursiveDir)%(FileName)%(Extension)$(_DeploymentFileMappingExtension)')"
A0A0A0A0A0A0A0A0A0A0A0 SkipUnchangedFiles="true"/>
A0
A0A0A0A0A0A0A0 <Copy
A0A0A0A0A0A0A0A0A0A0A0 SourceFiles="@(_DeploymentManifestDependencies)"
A0A0A0A0A0A0A0A0A0A0A0 DestinationFiles="@(_DeploymentManifestDependencies->
'$(_DeploymentApplicationDir)%(TargetPath)$(_DeploymentFileMappingExtension)')"
A0A0A0A0A0A0A0A0A0A0A0 SkipUnchangedFiles="true"
A0A0A0A0A0A0A0A0A0A0A0 Condition="'%(_DeploymentManifestDependencies.DependencyType)'=='Install'"/>
A0A0A0A0A0A0A0 <Copy
A0A0A0A0A0A0A0A0A0A0A0 SourceFiles="@(_ReferenceScatterPaths)"
A0A0A0A0A0A0A0A0A0A0A0 DestinationFiles="@(_ReferenceScatterPaths->
'$(_DeploymentApplicationDir)%(Filename)%(Extension)$(_DeploymentFileMappingExtension)')"
A0A0A0A0A0A0A0A0A0A0A0 SkipUnchangedFiles="true"/>
A0A0A0A0A0A0A0 <FormatUrl InputUrl="$(_DeploymentApplicationUrl)">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="OutputUrl" PropertyName="_DeploymentFormattedApplicationUrl"/>
A0A0A0A0A0A0A0 </FormatUrl>
A0A0A0A0A0A0A0 <FormatUrl InputUrl="$(_DeploymentComponentsUrl)">
A0A0A0A0A0A0A0A0A0A0A0 <Output TaskParameter="OutputUrl" PropertyName="_DeploymentFormattedComponentsUrl"/>
A0A0A0A0A0A0A0 </FormatUrl>
A0A0A0 </Target>
Finally you need include the new targets in your project, open your csproj file with a text editor and include the following line before the </Project> end tag.
A0 <Import Project="Customized.targets" />
The next time you publish the project you will see all assemblies and files inside the published directory.