diff --git a/cli.slnf b/cli.slnf
index e487d67ba499..a3ecb6ff2ed3 100644
--- a/cli.slnf
+++ b/cli.slnf
@@ -7,6 +7,7 @@
       "src\\Cli\\dn\\dn-native-debug.vcxproj",
       "src\\Cli\\dotnet\\dotnet.csproj",
       "src\\Cli\\Microsoft.DotNet.Cli.Utils\\Microsoft.DotNet.Cli.Utils.csproj",
+      "src\\Microsoft.DotNet.ProjectTools\\Microsoft.DotNet.ProjectTools.csproj",
       "test\\dotnet-new.IntegrationTests\\dotnet-new.IntegrationTests.csproj",
       "test\\dotnet-watch.Tests\\dotnet-watch.Tests.csproj",
       "test\\dotnet-aot.Tests\\dotnet-aot.Tests.csproj",
diff --git a/documentation/general/dotnet-run-file.md b/documentation/general/dotnet-run-file.md
index 1a09f48040ce..ce49aa4bce06 100644
--- a/documentation/general/dotnet-run-file.md
+++ b/documentation/general/dotnet-run-file.md
@@ -235,7 +235,7 @@ The directives are processed as follows:
 - Each `#:include` is injected as `<{1} Include="{0}" />` in an `<ItemGroup>`
   where `{0}` is the directive's value and `{1}` is determined by its extension.
   The mapping can be customized by setting the MSBuild property `FileBasedProgramsItemMapping`
-  which is by default set to `.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content`.
+  which is by default set to `.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content;.dll=Reference`.
 
   It is an error if the value is empty.
 
diff --git a/src/Cli/Microsoft.DotNet.FileBasedPrograms/FileLevelDirectiveHelpers.cs b/src/Cli/Microsoft.DotNet.FileBasedPrograms/FileLevelDirectiveHelpers.cs
index c038e131e753..9d4e7fb64f93 100644
--- a/src/Cli/Microsoft.DotNet.FileBasedPrograms/FileLevelDirectiveHelpers.cs
+++ b/src/Cli/Microsoft.DotNet.FileBasedPrograms/FileLevelDirectiveHelpers.cs
@@ -692,7 +692,7 @@ public sealed class IncludeOrExclude(in ParseInfo info) : Named(info)
     {
         public const string MappingPropertyName = "FileBasedProgramsItemMapping";
 
-        public static string DefaultMappingString => ".cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content";
+        public static string DefaultMappingString => ".cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content;.dll=Reference";
 
         public static ImmutableArray<(string Extension, string ItemType)> DefaultMapping
         {
@@ -706,6 +706,7 @@ public sealed class IncludeOrExclude(in ParseInfo info) : Named(info)
                         (".resx", "EmbeddedResource"),
                         (".json", "None"),
                         (".razor", "Content"),
+                        (".dll", "Reference"),
                     ];
                 }
 
@@ -833,7 +834,7 @@ public string KindToMSBuildString()
             SourceFile sourceFile,
             ErrorReporter errorReporter)
         {
-            var pairs = value.Split(';');
+            var pairs = value.Split([';'], StringSplitOptions.RemoveEmptyEntries);
 
             var builder = ImmutableArray.CreateBuilder<(string Extension, string ItemType)>(pairs.Length);
 
diff --git a/test/dotnet.Tests/CommandTests/Project/Convert/DotnetProjectConvertTests.cs b/test/dotnet.Tests/CommandTests/Project/Convert/DotnetProjectConvertTests.cs
index 59a31b2d8d38..f51472c02f8e 100644
--- a/test/dotnet.Tests/CommandTests/Project/Convert/DotnetProjectConvertTests.cs
+++ b/test/dotnet.Tests/CommandTests/Project/Convert/DotnetProjectConvertTests.cs
@@ -1821,7 +1821,6 @@ public static class LibClass
         var libDllProjectPath = Path.Join("Lib", "bin", "Debug", ToolsetInfo.CurrentTargetFramework, "Lib.dll");
 
         File.WriteAllText(Path.Join(testInstance.Path, "Program.cs"), $$"""
-            #:property FileBasedProgramsItemMapping=.dll=Reference
             #:include {{libDllDirectivePath}}
             Console.WriteLine(Lib.LibClass.GetMessage());
             """);
@@ -1851,7 +1850,6 @@ public static class LibClass
                     <PublishAot>true</PublishAot>
                     <PackAsTool>true</PackAsTool>
                     <UserSecretsId>Program-*</UserSecretsId>
-                    <FileBasedProgramsItemMapping>.dll=Reference</FileBasedProgramsItemMapping>
                   </PropertyGroup>
 
                   <ItemGroup>
@@ -1908,7 +1906,6 @@ public static class LibClass
             Path.Join(testInstance.Path, "Lib.dll"));
 
         File.WriteAllText(Path.Join(testInstance.Path, "Program.cs"), """
-            #:property FileBasedProgramsItemMapping=.dll=Reference
             #:include *.dll
             Console.WriteLine(Lib.LibClass.GetMessage());
             """);
@@ -1976,6 +1973,9 @@ public static class LibClass
 
         File.WriteAllText(Path.Join(srcDir, "Directory.Build.props"), $"""
             <Project>
+              <PropertyGroup>
+                <{CSharpDirective.IncludeOrExclude.MappingPropertyName}></{CSharpDirective.IncludeOrExclude.MappingPropertyName}>
+              </PropertyGroup>
               <ItemGroup>
                 <Reference Include="$(MSBuildThisFileDirectory){libDllPropsPath}" />
               </ItemGroup>
@@ -2050,9 +2050,6 @@ public static class LibClass
 
         File.WriteAllText(Path.Join(srcDir, "Directory.Build.props"), $"""
             <Project>
-              <PropertyGroup>
-                <FileBasedProgramsItemMapping>.dll=Reference</FileBasedProgramsItemMapping>
-              </PropertyGroup>
               <ItemGroup>
                 <Reference Include="$(MSBuildThisFileDirectory){libDllPropsPath}" />
               </ItemGroup>
@@ -2121,7 +2118,6 @@ public static class LibClass
         var libDllProjectPath = Path.Join("Lib", "bin", "Debug", ToolsetInfo.CurrentTargetFramework, "Lib.dll");
 
         File.WriteAllText(Path.Join(testInstance.Path, "extra.cs"), $$"""
-            #:property FileBasedProgramsItemMapping=.dll=Reference
             #:include {{libDllDirectivePath}}
             """);
 
@@ -2201,7 +2197,6 @@ public static class DependencyClass
 
         File.WriteAllText(Path.Join(libDir, "lib.cs"), $$"""
             #:property OutputType=Library
-            #:property FileBasedProgramsItemMapping=.dll=Reference
             #:include {{dependencyDllDirectivePath}}
             namespace MyLib;
             public static class Wrapper
diff --git a/test/dotnet.Tests/CommandTests/Run/RunFileTests_CscOnlyAndApi.cs b/test/dotnet.Tests/CommandTests/Run/RunFileTests_CscOnlyAndApi.cs
index 17455ae98aeb..6a6e377c79cd 100644
--- a/test/dotnet.Tests/CommandTests/Run/RunFileTests_CscOnlyAndApi.cs
+++ b/test/dotnet.Tests/CommandTests/Run/RunFileTests_CscOnlyAndApi.cs
@@ -1362,7 +1362,7 @@ public void Api()
                         <PackageOutputPath>artifacts/$(AssemblyName)</PackageOutputPath>
                         <FileBasedProgram>true</FileBasedProgram>
                         <EntryPointFilePath>{programPath}</EntryPointFilePath>
-                        <FileBasedProgramsItemMapping>.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content</FileBasedProgramsItemMapping>
+                        <FileBasedProgramsItemMapping>.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content;.dll=Reference</FileBasedProgramsItemMapping>
                         <EnableDefaultCompileItems>false</EnableDefaultCompileItems>
                         <DisableDefaultItemsInProjectFolder>true</DisableDefaultItemsInProjectFolder>
                         <OutputType>Exe</OutputType>
@@ -1447,7 +1447,7 @@ public void Api_Evaluation()
                         <PackageOutputPath>artifacts/$(AssemblyName)</PackageOutputPath>
                         <FileBasedProgram>true</FileBasedProgram>
                         <EntryPointFilePath>{programPath}</EntryPointFilePath>
-                        <FileBasedProgramsItemMapping>.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content</FileBasedProgramsItemMapping>
+                        <FileBasedProgramsItemMapping>.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content;.dll=Reference</FileBasedProgramsItemMapping>
                         <EnableDefaultCompileItems>false</EnableDefaultCompileItems>
                         <DisableDefaultItemsInProjectFolder>true</DisableDefaultItemsInProjectFolder>
                         <EnableDefaultEmbeddedResourceItems>false</EnableDefaultEmbeddedResourceItems>
@@ -1523,7 +1523,7 @@ public void Api_Diagnostic_01()
                         <PackageOutputPath>artifacts/$(AssemblyName)</PackageOutputPath>
                         <FileBasedProgram>true</FileBasedProgram>
                         <EntryPointFilePath>{programPath}</EntryPointFilePath>
-                        <FileBasedProgramsItemMapping>.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content</FileBasedProgramsItemMapping>
+                        <FileBasedProgramsItemMapping>.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content;.dll=Reference</FileBasedProgramsItemMapping>
                         <EnableDefaultCompileItems>false</EnableDefaultCompileItems>
                         <DisableDefaultItemsInProjectFolder>true</DisableDefaultItemsInProjectFolder>
                         <EnableDefaultEmbeddedResourceItems>false</EnableDefaultEmbeddedResourceItems>
@@ -1598,7 +1598,7 @@ public void Api_Diagnostic_02()
                         <PackageOutputPath>artifacts/$(AssemblyName)</PackageOutputPath>
                         <FileBasedProgram>true</FileBasedProgram>
                         <EntryPointFilePath>{programPath}</EntryPointFilePath>
-                        <FileBasedProgramsItemMapping>.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content</FileBasedProgramsItemMapping>
+                        <FileBasedProgramsItemMapping>.cs=Compile;.resx=EmbeddedResource;.json=None;.razor=Content;.dll=Reference</FileBasedProgramsItemMapping>
                         <EnableDefaultCompileItems>false</EnableDefaultCompileItems>
                         <DisableDefaultItemsInProjectFolder>true</DisableDefaultItemsInProjectFolder>
                         <EnableDefaultEmbeddedResourceItems>false</EnableDefaultEmbeddedResourceItems>