Changing multiple dotnet commands to be aware of $configuration/$tfm folder structure under the --output path option.

Changing the build scripts to copy files over from debug\dnxcore and to check for the folders existence before trying that.
Making the build command aware of the subfolders and making E2E tests aware of subfolders.
Fixing compiler tests to look for the xml in the right plae taking into consideration the configuration and tfm.
Modifying publish tests to not take into consideration the runtime. This is a temporary change. will bring it back once the commands all understand rid.
Making the packaging step work by placing binaries where dotnet pack expects.

test/Microsoft.DotNet.Tools.Tests.Utilities/TestBase.cs

@@ -58,9 +58,13 @@ namespace Microsoft.DotNet.Tools.Test.Utilities
                 string.Equals("on", val, StringComparison.OrdinalIgnoreCase));
         }
 
-        protected void TestOutputExecutable(string outputDir, string executableName, string expectedOutput)
+        protected void TestOutputExecutable(
+            string outputDir,
+            string executableName,
+            string expectedOutput,
+            bool native = false)
         {
-            var executablePath = Path.Combine(outputDir, executableName);
+            var executablePath = Path.Combine(GetBinariesOutputDirectory(outputDir, native), executableName);
 
             var executableCommand = new TestCommand(executablePath);
 
@@ -70,5 +74,21 @@ namespace Microsoft.DotNet.Tools.Test.Utilities
             result.Should().NotHaveStdErr();
             result.Should().Pass();
         }
+
+        private void TestNativeOutputExecutable(string outputDir, string executableName, string expectedOutput)
+        {
+            TestOutputExecutable(outputDir, executableName, expectedOutput, true);
+        }
+
+        private string GetBinariesOutputDirectory(string outputDir, bool native)
+        {
+            var executablePath = Path.Combine(outputDir, "Debug", "dnxcore50");
+            if (native)
+            {
+                executablePath = Path.Combine(outputDir, "Debug", "dnxcore50", "native");
+            }
+
+            return executablePath;
+        }
     }
 }