diff --git a/build.proj b/build.proj
index 887061871..f0d06e0cc 100644
--- a/build.proj
+++ b/build.proj
@@ -1,8 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
 <Project ToolsVersion="14.0" DefaultTargets="BuildTheWholeCli" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <Import Project="build/Microsoft.DotNet.Cli.Prepare.targets" />
-  <Import Project="build/Microsoft.DotNet.Cli.Compile.targets" />
-
   <PropertyGroup>
     <!--
       $(OS) is set to Unix/Windows_NT. This comes from an environment variable on Windows and MSBuild on Unix.
@@ -72,4 +69,5 @@
 
   <Import Project="build/Microsoft.DotNet.Cli.Prepare.targets" />
   <Import Project="build/Microsoft.DotNet.Cli.Package.targets" />
+  <Import Project="build/Microsoft.DotNet.Cli.Compile.targets" />
 </Project>
diff --git a/build/Microsoft.DotNet.Cli.Compile.targets b/build/Microsoft.DotNet.Cli.Compile.targets
index 299152f19..f2fb8b5d0 100644
--- a/build/Microsoft.DotNet.Cli.Compile.targets
+++ b/build/Microsoft.DotNet.Cli.Compile.targets
@@ -14,7 +14,8 @@
     </Target>
 
     <Target Name="CompileStage1"
-            DependsOnTargets="Init;
+            DependsOnTargets="BuildDotnetCliBuildFramework;
+                              Init;
                               SetupStage1;
                               CompileStage;
                               AfterCompileStage">   
@@ -29,7 +30,8 @@
     </Target>    
 
     <Target Name="CompileStage2"
-            DependsOnTargets="Init;
+            DependsOnTargets="BuildDotnetCliBuildFramework;
+                              Init;
                               SetupStage2;
                               CompileStage;
                               AfterCompileStage;
@@ -103,7 +105,7 @@
               DepsFile="$(SdkOutputDirectory)/csc.deps.json"
               NewName="csc.deps.json" />
 
-        <RemoveAssetFromDepsPackages DepsFile="$(BinaryToCorehostifyRelDir)/csc.deps.json"
+        <RemoveAssetFromDepsPackages DepsFile="$(SdkOutputDirectory)/csc.deps.json"
                                      SectionName="runtimeTargets"
                                      AssetPath="$(BinaryToCorehostifyRelDir)/%(BinariesToRemove.Identity).exe" />
         <RemoveAssetFromDepsPackages DepsFile="$(SdkOutputDirectory)/dotnet.deps.json"
@@ -160,6 +162,7 @@
         <ItemGroup>
           <BinObj Include="$(SrcDirectory)/**/bin/**/*" />
           <BinObj Include="$(SrcDirectory)/**/obj/**/*" />
+          <FilesToRemoveFromStageDirectory Include="$(StageDirectory)/**/*" />
         </ItemGroup>        
 
         <SharedFrameworkNameVersionPath RootOutputDirectory="$(StageDirectory)">
@@ -168,22 +171,29 @@
 
         <Delete Files="@(BinObj)" />
 
+        <Delete Files="@(FilesToRemoveFromStageDirectory)" />
         <RemoveDir Directories="$(StageDirectory)" />
         <MakeDir Directories="$(StageDirectory)"/>      
     </Target>
 
-    <Target Name="AfterCompileStage">
+    <Target Name="AfterCompileStage"
+            DependsOnTargets="RemoveUnnecessaryFiles">
         <ItemGroup>
-            <FilesToClean Include="$(StageDirectory)/sdk/**/vbc.exe" />
             <FilesToCopy Include="$(StageDirectory)/**/*.*" />
             <PdbsToClean Include="$(StageDirectory)/sdk/**/*.pdb" />
         </ItemGroup>
 
-        <Delete Files="@(FilesToClean)" />
-
         <Copy SourceFiles="@(FilesToCopy)"
             DestinationFiles="@(FilesToCopy->'$(StageSymbolsDirectory)\%(RecursiveDir)%(Filename)%(Extension)')" />
 
         <Delete Files="@(PdbsToClean)" />
     </Target>
+
+    <Target Name="RemoveUnnecessaryFiles">
+        <ItemGroup>
+            <FilesToClean Include="$(StageDirectory)/sdk/**/vbc.exe" />
+        </ItemGroup>
+
+        <Delete Files="@(FilesToClean)" />
+    </Target>
 </Project>
\ No newline at end of file
diff --git a/build/compile/Microsoft.DotNet.Cli.Archive.targets b/build/compile/Microsoft.DotNet.Cli.Archive.targets
index f52d76cfc..ce8bb9240 100644
--- a/build/compile/Microsoft.DotNet.Cli.Archive.targets
+++ b/build/compile/Microsoft.DotNet.Cli.Archive.targets
@@ -9,6 +9,12 @@
 
     <Target Name="RestoreNuGetPackagesArchive"
             DependsOnTargets="SetupNuGetPackagesArchiveInputsOutputs">
+        <ItemGroup>
+            <FilesToClean Include="$(NuGetPackagesArchiveProject)/**/*" />
+            <FilesToClean Include="$(NuGetPackagesArchiveFolder)/**/*" />
+        </ItemGroup>
+
+        <Delete Files="@(FilesToClean)" />
         <RemoveDir Directories="$(NuGetPackagesArchiveProject);$(NuGetPackagesArchiveFolder)" />
         <MakeDir Directories="$(NuGetPackagesArchiveProject);$(NuGetPackagesArchiveFolder)"/>
 
diff --git a/build/package/Microsoft.DotNet.Cli.Nupkg.targets b/build/package/Microsoft.DotNet.Cli.Nupkg.targets
index 3a888ce60..99f667dc0 100644
--- a/build/package/Microsoft.DotNet.Cli.Nupkg.targets
+++ b/build/package/Microsoft.DotNet.Cli.Nupkg.targets
@@ -69,7 +69,8 @@
   </Target>
 
   <Target Name="BuildProjectsForNuGetPackages"
-            DependsOnTargets="Init"            
+            DependsOnTargets="Init;
+                              SetupGenerateNugetPackagesInputsOutputs"            
             Condition=" '$(OS)' == 'Windows_NT' ">
         <MakeDir Directories="$(PackagingBuildBasePath)" />