Clean should delete the generated Files

sample/FunctionApp/FunctionApp/FunctionApp.csproj

@@ -5,7 +5,7 @@
   <ItemGroup>
     <PackageReference Include="Microsoft.Azure.WebJobs" Version="2.1.0-beta1" />
     <PackageReference Include="Microsoft.Azure.WebJobs.Extensions.Http" Version="1.0.0-beta1" />
-    <PackageReference Include="Microsoft.NET.Sdk.Functions" Version="1.0.0-alpha7" />
+    <PackageReference Include="Microsoft.NET.Sdk.Functions" Version="1.0.0" />
   </ItemGroup>
   <ItemGroup>
     <Reference Include="Microsoft.CSharp" />

src/Microsoft.NET.Sdk.Functions/Microsoft.NET.Sdk.Functions.csproj

@@ -2,7 +2,7 @@
 
   <PropertyGroup>
     <TargetFrameworks>netstandard1.5;net46</TargetFrameworks>
-    <PackageVersion>1.0.0-alpha7</PackageVersion>
+    <PackageVersion>1.0.0</PackageVersion>
     <BuildOutputTargetFolder>tools</BuildOutputTargetFolder>
     <AssemblyOriginatorKeyFile>PublicKey.snk</AssemblyOriginatorKeyFile>
     <SignAssembly>False</SignAssembly>

src/Microsoft.NET.Sdk.Functions/Targets/netstandard1.0/Microsoft.NET.Sdk.Functions.targets

@@ -138,4 +138,88 @@ Copyright (c) .NET Foundation. All rights reserved.
       OutputPath="$(PublishIntermediateOutputPath)"/>
   </Target>
 
+  <!--********************************************************************-->
+  <!-- CopyLocalLockFileAssemblies does not copy all the required assemblies 
+       to the bin folder. These adhoc targets fixes the issue.
+                                                                          -->
+  <!--********************************************************************-->
+
+  <Target
+   Name="ResolveAdditionalReferenceCopyLocalPathsForFunctions"
+   DependsOnTargets="RunResolvePublishAssembliesForFunctions"
+   AfterTargets="ResolveReferences"
+     >
+
+    <!--
+      Copy publish assemblies that not already included in ReferenceCopyLocalPaths
+      via CopyLocalLockFileAssemblies=true. This will include RID-specific assets 
+      that would be published in  the runtimes/ folder, but excluded from 
+      CopyLocalLockFileAssemblies when no RuntimeIdentifier is set.
+    -->
+    <ItemGroup Condition="'$(RuntimeIdentifier)' == ''">
+      <!-- 
+       NOTE: The exclusion here is to ensure that we do not override any existing 
+             ReferenceCopyLocalPaths with assets from RunResolvedPublishAssemblies.
+             The ReferenceCopyLocalPaths can have conflicts resolved that are not 
+             also resolved in the publish set, and publish currently relies on copy
+             local paths having precedence over it to ensure conflict resolution 
+             applies. We must preserve that precedence here.
+     -->
+      <_RidSpecificAssembliesByDestination
+        Include="@(ResolvedAssembliesToPublish->'%(DestinationSubPath)')"
+        Exclude="@(ReferenceCopyLocalPaths->'%(DestinationSubDirectory)%(Filename)%(Extension)')"
+        OriginalItemSpec="%(ResolvedAssembliesToPublish.Identity)"
+       />
+
+      <_RidSpecificAssembliesByDestination
+        DestinationSubDirectory="%(_RidSpecificAssembliesByDestination.RelativeDir)"
+       />
+
+      <ReferenceCopyLocalPaths
+        Include="@(_RidSpecificAssembliesByDestination->'%(OriginalItemSpec)')"
+        Exclude="@(ReferenceCopyLocalPaths)"
+       />
+    </ItemGroup>
+
+    <!--
+       Copy reference assemblies needed for runtime compilation to refs/ folder. Only 
+       those that are not a also runtime assemblies and therefore already included in 
+       ReferenceCopyLocalPaths via CopyLocalLockFileAssemblies=true are needed.
+      -->
+    <ItemGroup Condition="'$(PreserveCompilationContext)' == 'true'">
+      <ReferenceCopyLocalPaths
+        Include="@(ReferencePath)"
+        Exclude="@(ReferenceCopyLocalPaths)"
+        DestinationSubDirectory="$(RefAssembliesFolderName)\"
+        />
+    </ItemGroup>
+
+  </Target>
+
+  <!-- 
+     We only need to call RunResolvePublishAssemblies during build when we do not 
+     have a RuntimeIdentifier.Otherwise, we already have everything we need from
+     CopyLocalLockFileAssemblies.
+   -->
+  <Target
+    Name="RunResolvePublishAssembliesForFunctions"
+    Condition="'$(RuntimeIdentifier)' == ''"
+    DependsOnTargets="RunResolvePublishAssemblies"
+  />
+
+  <!-- 
+     Cleanup the TargetDir folder on Clean to delete the generated content.
+   -->
+  <Target
+    Name="CleanupTargetDir"
+    AfterTargets="Clean">
+
+    <ItemGroup>
+      <_FilesInTargetDir Include="$(TargetDir)\**\*" />
+    </ItemGroup>
+
+    <Delete Files="@(_FilesInTargetDir)" ContinueOnError="true" />
+    <RemoveDir Directories="$(TargetDir)" ContinueOnError="true" />  
+  </Target>
+  
 </Project>