diff --git a/src/Tgstation.Server.Host/Components/StaticFiles/Configuration.cs b/src/Tgstation.Server.Host/Components/StaticFiles/Configuration.cs
index 6e80a0c475..350d701880 100644
--- a/src/Tgstation.Server.Host/Components/StaticFiles/Configuration.cs
+++ b/src/Tgstation.Server.Host/Components/StaticFiles/Configuration.cs
@@ -57,6 +57,16 @@ namespace Tgstation.Server.Host.Components.StaticFiles
 		/// </summary>
 		const string CodeModificationsTailFile = "TailInclude.dm";
 
+		/// <summary>
+		/// Default contents of <see cref="CodeModificationsHeadFile"/>.
+		/// </summary>
+		static readonly string DefaultHeadInclude = @$"// TGS AUTO GENERATED HeadInclude.dm{Environment.NewLine}// This file will be included BEFORE all code in your .dme IF a replacement .dme does not exist in this directory{Environment.NewLine}// Please note that changes need to be made available if you are hosting an AGPL licensed codebase{Environment.NewLine}// The presence file in its default state does not constitute a code change that needs to be published by licensing standards{Environment.NewLine}";
+
+		/// <summary>
+		/// Default contents of <see cref="CodeModificationsHeadFile"/>.
+		/// </summary>
+		static readonly string DefaultTailInclude = @$"// TGS AUTO GENERATED TailInclude.dm{Environment.NewLine}// This file will be included AFTER all code in your .dme IF a replacement .dme does not exist in this directory{Environment.NewLine}// Please note that changes need to be made available if you are hosting an AGPL licensed codebase{Environment.NewLine}// The presence file in its default state does not constitute a code change that needs to be published by licensing standards{Environment.NewLine}";
+
 		/// <summary>
 		/// Map of <see cref="EventType"/>s to the filename of the event scripts they trigger.
 		/// </summary>
@@ -648,8 +658,29 @@ namespace Tgstation.Server.Host.Components.StaticFiles
 					await ioManager.WriteAllBytes(staticIgnorePath, Array.Empty<byte>(), cancellationToken);
 			}
 
+			async Task ValidateCodeModsFolder()
+			{
+				if (await ioManager.DirectoryExists(CodeModificationsSubdirectory, cancellationToken))
+					return;
+
+				await ioManager.CreateDirectory(CodeModificationsSubdirectory, cancellationToken);
+				await Task.WhenAll(
+					ioManager.WriteAllBytes(
+						ioManager.ConcatPath(
+							CodeModificationsSubdirectory,
+							CodeModificationsHeadFile),
+						Encoding.UTF8.GetBytes(DefaultHeadInclude),
+						cancellationToken),
+					ioManager.WriteAllBytes(
+						ioManager.ConcatPath(
+							CodeModificationsSubdirectory,
+							CodeModificationsTailFile),
+						Encoding.UTF8.GetBytes(DefaultTailInclude),
+						cancellationToken));
+			}
+
 			await Task.WhenAll(
-				ioManager.CreateDirectory(CodeModificationsSubdirectory, cancellationToken),
+				ValidateCodeModsFolder(),
 				ioManager.CreateDirectory(EventScriptsSubdirectory, cancellationToken),
 				ValidateStaticFolder());
 		}
diff --git a/tests/Tgstation.Server.Tests/Live/Instance/ConfigurationTest.cs b/tests/Tgstation.Server.Tests/Live/Instance/ConfigurationTest.cs
index ac5ce72067..8a7c7013c1 100644
--- a/tests/Tgstation.Server.Tests/Live/Instance/ConfigurationTest.cs
+++ b/tests/Tgstation.Server.Tests/Live/Instance/ConfigurationTest.cs
@@ -119,9 +119,32 @@ namespace Tgstation.Server.Tests.Live.Instance
 				);
 		}
 
+		Task TestPregeneratedFilesExist(CancellationToken cancellationToken) => Task.Factory.StartNew(
+			_ =>
+			{
+				var configDir = Path.Combine(instance.Path, "Configuration");
+				var baseDir = Path.Combine(configDir, "CodeModifications");
+				var path = Path.Combine(baseDir, "HeadInclude.dm");
+				var result = File.Exists(path);
+				Assert.IsTrue(result);
+				path = Path.Combine(baseDir, "TailInclude.dm");
+				result = File.Exists(path);
+				Assert.IsTrue(result);
+				var tgsIgnore = Path.Combine(configDir, "GameStaticFiles", ".tgsignore");
+				result = File.Exists(tgsIgnore);
+				Assert.IsTrue(result);
+			},
+			null,
+			cancellationToken,
+			TaskCreationOptions.LongRunning,
+			TaskScheduler.Current);
+
 		public Task RunPreWatchdog(CancellationToken cancellationToken)
 		{
-			return Task.WhenAll(TestUploadDownloadAndDeleteDirectory(cancellationToken), SetupDMApiTests(cancellationToken));
+			return Task.WhenAll(
+				TestUploadDownloadAndDeleteDirectory(cancellationToken),
+				SetupDMApiTests(cancellationToken),
+				TestPregeneratedFilesExist(cancellationToken));
 		}
 	}
 }
diff --git a/tests/Tgstation.Server.Tests/Live/Instance/InstanceTest.cs b/tests/Tgstation.Server.Tests/Live/Instance/InstanceTest.cs
index 63b8798223..b30533f082 100644
--- a/tests/Tgstation.Server.Tests/Live/Instance/InstanceTest.cs
+++ b/tests/Tgstation.Server.Tests/Live/Instance/InstanceTest.cs
@@ -26,7 +26,7 @@ namespace Tgstation.Server.Tests.Live.Instance
 			this.serverPort = serverPort;
 		}
 
-		public async Task RunTests(CancellationToken cancellationToken, bool highPrioDD, bool lowPrioDeployment)
+		public async Task RunTests(bool highPrioDD, bool lowPrioDeployment, CancellationToken cancellationToken)
 		{
 			var byondTest = new ByondTest(instanceClient.Byond, instanceClient.Jobs, fileDownloader, instanceClient.Metadata);
 			var chatTest = new ChatTest(instanceClient.ChatBots, instanceManagerClient, instanceClient.Jobs, instanceClient.Metadata);
diff --git a/tests/Tgstation.Server.Tests/Live/Instance/RepositoryTest.cs b/tests/Tgstation.Server.Tests/Live/Instance/RepositoryTest.cs
index 05f3b90ec2..8fb677a8e4 100644
--- a/tests/Tgstation.Server.Tests/Live/Instance/RepositoryTest.cs
+++ b/tests/Tgstation.Server.Tests/Live/Instance/RepositoryTest.cs
@@ -40,6 +40,7 @@ namespace Tgstation.Server.Tests.Live.Instance
 
 			async Task<JobResponse> Rest()
 			{
+				await Task.Yield();
 				await ApiAssert.ThrowsException<ConflictException>(() => repositoryClient.Read(cancellationToken), ErrorCode.RepoCloning);
 				Assert.IsNotNull(clone);
 				Assert.AreEqual(cloneRequest.Origin, clone.Origin);
diff --git a/tests/Tgstation.Server.Tests/Live/TestLiveServer.cs b/tests/Tgstation.Server.Tests/Live/TestLiveServer.cs
index b24538b125..47afd08b2b 100644
--- a/tests/Tgstation.Server.Tests/Live/TestLiveServer.cs
+++ b/tests/Tgstation.Server.Tests/Live/TestLiveServer.cs
@@ -1052,9 +1052,9 @@ namespace Tgstation.Server.Tests.Live
 							GetInstanceManager(),
 							(ushort)server.Url.Port)
 						.RunTests(
-							cancellationToken,
 							server.HighPriorityDreamDaemon,
-							server.LowPriorityDeployments));
+							server.LowPriorityDeployments,
+							cancellationToken));
 
 					await Task.WhenAll(rootTest, adminTest, instancesTest, instanceTests, usersTest);