diff --git a/README.md b/README.md
index fc51052f..b5ffc111 100644
--- a/README.md
+++ b/README.md
@@ -83,7 +83,7 @@ Once you've done some work on the first branch within the stack, at some point y
 - Give the branch a name.
 - Select the branch to create the new branch from.
 
-The new branch will be created from the branch at the bottom of the stack and the current branch will be changed so you can make more changes.
+The new branch will be created from the selected parent branch and the current branch will be changed so you can make more changes.
 
 If a new branch was not able to be pushed to the remote, you can use the `stack push` command to push the branch to the remote later.
 
diff --git a/src/Stack.Tests/Commands/Branch/AddBranchCommandHandlerTests.cs b/src/Stack.Tests/Commands/Branch/AddBranchCommandHandlerTests.cs
index 4c745f9d..dd7f036c 100644
--- a/src/Stack.Tests/Commands/Branch/AddBranchCommandHandlerTests.cs
+++ b/src/Stack.Tests/Commands/Branch/AddBranchCommandHandlerTests.cs
@@ -13,41 +13,46 @@ namespace Stack.Tests.Commands.Branch;
 public class AddBranchCommandHandlerTests(ITestOutputHelper testOutputHelper)
 {
     [Fact]
-    public async Task WhenNoInputsProvided_AsksForStackAndBranchAndConfirms_AddsBranchToStack()
+    public async Task WhenNoInputsProvided_AsksForStackAndBranchAndParentBranchAndConfirms_AddsBranchToStack()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
-        var anotherBranch = Some.BranchName();
+        var firstBranch = Some.BranchName();
+        var childBranch = Some.BranchName();
         var branchToAdd = Some.BranchName();
         var remoteUri = Some.HttpsUri().ToString();
 
-        var stackConfig = new TestStackConfigBuilder()
-            .WithStack(stack => stack
-                .WithName("Stack1")
-                .WithRemoteUri(remoteUri)
-                .WithSourceBranch(sourceBranch)
-                .WithBranch(branch => branch.WithName(anotherBranch)))
-            .WithStack(stack => stack.WithName("Stack2").WithRemoteUri(remoteUri).WithSourceBranch(sourceBranch))
-            .Build();
         var inputProvider = Substitute.For<IInputProvider>();
         var logger = new TestLogger(testOutputHelper);
         var gitClient = Substitute.For<IGitClient>();
         gitClient.GetRemoteUri().Returns(remoteUri);
         gitClient.GetCurrentBranch().Returns(sourceBranch);
-        gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, anotherBranch, branchToAdd });
+        gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, firstBranch, childBranch, branchToAdd });
         gitClient.DoesLocalBranchExist(branchToAdd).Returns(true);
+        var stackConfig = new TestStackConfigBuilder()
+            .WithStack(stack => stack
+                .WithName("Stack1")
+                .WithRemoteUri(remoteUri)
+                .WithSourceBranch(sourceBranch)
+                .WithBranch(branch => branch.WithName(firstBranch).WithChildBranch(child => child.WithName(childBranch))))
+            .WithStack(stack => stack
+                .WithName("Stack2")
+                .WithRemoteUri(remoteUri)
+                .WithSourceBranch(sourceBranch))
+            .Build();
         var handler = new AddBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
 
         inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
         inputProvider.Select(Questions.SelectBranch, Arg.Any<string[]>()).Returns(branchToAdd);
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(firstBranch);
 
         // Act
-        await handler.Handle(AddBranchCommandInputs.Empty);
+        await handler.Handle(new AddBranchCommandInputs(null, null, null));
 
         // Assert
         stackConfig.Stacks.Should().BeEquivalentTo(new List<Config.Stack>
         {
-            new("Stack1", remoteUri, sourceBranch, [new Config.Branch(anotherBranch, [new Config.Branch(branchToAdd, [])])]),
+            new("Stack1", remoteUri, sourceBranch, [new Config.Branch(firstBranch, [new Config.Branch(childBranch, []), new Config.Branch(branchToAdd, [])])]),
             new("Stack2", remoteUri, sourceBranch, [])
         });
     }
@@ -79,6 +84,7 @@ public async Task WhenStackNameProvided_DoesNotAskForStackName_AddsBranchFromSta
         var handler = new AddBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
 
         inputProvider.Select(Questions.SelectBranch, Arg.Any<string[]>()).Returns(branchToAdd);
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(anotherBranch);
 
         // Act
         await handler.Handle(new AddBranchCommandInputs("Stack1", null, null));
@@ -118,6 +124,7 @@ public async Task WhenOnlyOneStackExists_DoesNotAskForStackName_AddsBranchFromSt
         var handler = new AddBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
 
         inputProvider.Select(Questions.SelectBranch, Arg.Any<string[]>()).Returns(branchToAdd);
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(anotherBranch);
 
         // Act
         await handler.Handle(new AddBranchCommandInputs(null, null, null));
@@ -191,6 +198,7 @@ public async Task WhenBranchNameProvided_DoesNotAskForBranchName_AddsBranchFromS
         var handler = new AddBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
 
         inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(anotherBranch);
 
         // Act
         await handler.Handle(new AddBranchCommandInputs(null, branchToAdd, null));
@@ -305,7 +313,7 @@ public async Task WhenAllInputsProvided_DoesNotAskForAnything_AddsBranchFromStac
         var handler = new AddBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
 
         // Act
-        await handler.Handle(new AddBranchCommandInputs("Stack1", branchToAdd, null));
+        await handler.Handle(new AddBranchCommandInputs("Stack1", branchToAdd, anotherBranch));
 
         // Assert
         stackConfig.Stacks.Should().BeEquivalentTo(new List<Config.Stack>
@@ -317,7 +325,7 @@ public async Task WhenAllInputsProvided_DoesNotAskForAnything_AddsBranchFromStac
     }
 
     [Fact]
-    public async Task WhenV2Schema_AndParentBranchNotProvided_AsksForParentBranch_CreatesNewBranchUnderneathParent()
+    public async Task WhenParentBranchProvided_DoesNotAskForParentBranch_CreatesNewBranchUnderneathParent()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
@@ -334,53 +342,6 @@ public async Task WhenV2Schema_AndParentBranchNotProvided_AsksForParentBranch_Cr
         gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, firstBranch, childBranch, branchToAdd });
         gitClient.DoesLocalBranchExist(branchToAdd).Returns(true);
         var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V2)
-            .WithStack(stack => stack
-                .WithName("Stack1")
-                .WithRemoteUri(remoteUri)
-                .WithSourceBranch(sourceBranch)
-                .WithBranch(branch => branch.WithName(firstBranch).WithChildBranch(child => child.WithName(childBranch))))
-            .WithStack(stack => stack
-                .WithName("Stack2")
-                .WithRemoteUri(remoteUri)
-                .WithSourceBranch(sourceBranch))
-            .Build();
-        var handler = new AddBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
-
-        inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
-        inputProvider.Select(Questions.SelectBranch, Arg.Any<string[]>()).Returns(branchToAdd);
-        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(firstBranch);
-
-        // Act
-        await handler.Handle(new AddBranchCommandInputs(null, null, null));
-
-        // Assert
-        stackConfig.Stacks.Should().BeEquivalentTo(new List<Config.Stack>
-        {
-            new("Stack1", remoteUri, sourceBranch, [new Config.Branch(firstBranch, [new Config.Branch(childBranch, []), new Config.Branch(branchToAdd, [])])]),
-            new("Stack2", remoteUri, sourceBranch, [])
-        });
-    }
-
-    [Fact]
-    public async Task WhenV2Schema_AndParentBranchProvided_DoesNotAskForParentBranch_CreatesNewBranchUnderneathParent()
-    {
-        // Arrange
-        var sourceBranch = Some.BranchName();
-        var firstBranch = Some.BranchName();
-        var childBranch = Some.BranchName();
-        var branchToAdd = Some.BranchName();
-        var remoteUri = Some.HttpsUri().ToString();
-
-        var inputProvider = Substitute.For<IInputProvider>();
-        var logger = new TestLogger(testOutputHelper);
-        var gitClient = Substitute.For<IGitClient>();
-        gitClient.GetRemoteUri().Returns(remoteUri);
-        gitClient.GetCurrentBranch().Returns(sourceBranch);
-        gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, firstBranch, childBranch, branchToAdd });
-        gitClient.DoesLocalBranchExist(branchToAdd).Returns(true);
-        var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V2)
             .WithStack(stack => stack
                 .WithName("Stack1")
                 .WithRemoteUri(remoteUri)
@@ -408,44 +369,4 @@ public async Task WhenV2Schema_AndParentBranchProvided_DoesNotAskForParentBranch
 
         inputProvider.DidNotReceive().Select(Questions.SelectParentBranch, Arg.Any<string[]>());
     }
-
-    [Fact]
-    public async Task WhenV1Schema_AndParentBranchProvided_ThrowsException()
-    {
-        // Arrange
-        var sourceBranch = Some.BranchName();
-        var firstBranch = Some.BranchName();
-        var childBranch = Some.BranchName();
-        var branchToAdd = Some.BranchName();
-        var remoteUri = Some.HttpsUri().ToString();
-
-        var inputProvider = Substitute.For<IInputProvider>();
-        var logger = new TestLogger(testOutputHelper);
-        var gitClient = Substitute.For<IGitClient>();
-        gitClient.GetRemoteUri().Returns(remoteUri);
-        gitClient.GetCurrentBranch().Returns(sourceBranch);
-        gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, firstBranch, childBranch, branchToAdd });
-        gitClient.DoesLocalBranchExist(branchToAdd).Returns(true);
-        var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V1)
-            .WithStack(stack => stack
-                .WithName("Stack1")
-                .WithRemoteUri(remoteUri)
-                .WithSourceBranch(sourceBranch)
-                .WithBranch(branch => branch.WithName(firstBranch).WithChildBranch(child => child.WithName(childBranch))))
-            .WithStack(stack => stack
-                .WithName("Stack2")
-                .WithRemoteUri(remoteUri)
-                .WithSourceBranch(sourceBranch))
-            .Build();
-        var handler = new AddBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
-
-        inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
-        inputProvider.Select(Questions.SelectBranch, Arg.Any<string[]>()).Returns(branchToAdd);
-
-        // Act and assert
-        await handler.Invoking(h => h.Handle(new AddBranchCommandInputs(null, null, firstBranch)))
-            .Should().ThrowAsync<InvalidOperationException>()
-            .WithMessage("Parent branches are not supported in stacks with schema version v1. Please migrate the stack to v2 format.");
-    }
 }
diff --git a/src/Stack.Tests/Commands/Branch/NewBranchCommandHandlerTests.cs b/src/Stack.Tests/Commands/Branch/NewBranchCommandHandlerTests.cs
index b18b0f83..32f04d37 100644
--- a/src/Stack.Tests/Commands/Branch/NewBranchCommandHandlerTests.cs
+++ b/src/Stack.Tests/Commands/Branch/NewBranchCommandHandlerTests.cs
@@ -13,11 +13,12 @@ namespace Stack.Tests.Commands.Branch;
 public class NewBranchCommandHandlerTests(ITestOutputHelper testOutputHelper)
 {
     [Fact]
-    public async Task WhenNoInputsProvided_AsksForStackAndBranch_CreatesAndAddsBranchToStack_PushesToRemote_AndSwitchesToBranch()
+    public async Task WhenNoInputsProvided_AsksForStackAndBranchAndParentBranch_CreatesAndAddsBranchToStack_PushesToRemote_AndSwitchesToBranch()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
-        var anotherBranch = Some.BranchName();
+        var firstBranch = Some.BranchName();
+        var childBranch = Some.BranchName();
         var newBranch = Some.BranchName();
         var remoteUri = Some.HttpsUri().ToString();
 
@@ -29,7 +30,7 @@ public async Task WhenNoInputsProvided_AsksForStackAndBranch_CreatesAndAddsBranc
                 .WithName("Stack1")
                 .WithRemoteUri(remoteUri)
                 .WithSourceBranch(sourceBranch)
-                .WithBranch(branch => branch.WithName(anotherBranch)))
+                .WithBranch(branch => branch.WithName(firstBranch).WithChildBranch(child => child.WithName(childBranch))))
             .WithStack(stack => stack
                 .WithName("Stack2")
                 .WithRemoteUri(remoteUri)
@@ -39,10 +40,10 @@ public async Task WhenNoInputsProvided_AsksForStackAndBranch_CreatesAndAddsBranc
 
         inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
         inputProvider.Text(Questions.BranchName, Arg.Any<string>()).Returns(newBranch);
-
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(firstBranch);
         gitClient.GetRemoteUri().Returns(remoteUri);
         gitClient.GetCurrentBranch().Returns(sourceBranch);
-        gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, anotherBranch });
+        gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, firstBranch, childBranch });
         gitClient.DoesLocalBranchExist(newBranch).Returns(false);
 
         // Act
@@ -51,11 +52,10 @@ public async Task WhenNoInputsProvided_AsksForStackAndBranch_CreatesAndAddsBranc
         // Assert
         stackConfig.Stacks.Should().BeEquivalentTo(new List<Config.Stack>
         {
-            new("Stack1", remoteUri, sourceBranch, [new Config.Branch(anotherBranch, [new Config.Branch(newBranch, [])])]),
+            new("Stack1", remoteUri, sourceBranch, [new Config.Branch(firstBranch, [new Config.Branch(childBranch, []), new Config.Branch(newBranch, [])])]),
             new("Stack2", remoteUri, sourceBranch, [])
         });
-        gitClient.Received().CreateNewBranch(newBranch, anotherBranch);
-        gitClient.Received().PushNewBranch(newBranch);
+        gitClient.Received().CreateNewBranch(newBranch, firstBranch);
         gitClient.Received().ChangeBranch(newBranch);
     }
 
@@ -85,6 +85,8 @@ public async Task WhenStackNameProvided_DoesNotAskForStackName_CreatesAndAddsBra
         var handler = new NewBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
 
         inputProvider.Text(Questions.BranchName, Arg.Any<string>()).Returns(newBranch);
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(anotherBranch);
+
         gitClient.GetRemoteUri().Returns(remoteUri);
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, anotherBranch });
@@ -124,6 +126,8 @@ public async Task WhenOnlyOneStackExists_DoesNotAskForStackName_CreatesAndAddsBr
         var handler = new NewBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
 
         inputProvider.Text(Questions.BranchName, Arg.Any<string>()).Returns(newBranch);
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(anotherBranch);
+
         gitClient.GetRemoteUri().Returns(remoteUri);
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, anotherBranch });
@@ -203,6 +207,8 @@ public async Task WhenBranchNameProvided_DoesNotAskForBranchName_CreatesAndAddsB
         var handler = new NewBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
 
         inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(anotherBranch);
+
         gitClient.GetRemoteUri().Returns(remoteUri);
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, anotherBranch });
@@ -325,6 +331,8 @@ public async Task WhenPushToTheRemoteFails_StillCreatesTheBranchLocallyAndAddsIt
 
         inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
         inputProvider.Text(Questions.BranchName, Arg.Any<string>()).Returns(newBranch);
+        inputProvider.Select(Questions.SelectParentBranch, Arg.Any<string[]>()).Returns(anotherBranch);
+
         gitClient.GetRemoteUri().Returns(remoteUri);
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, anotherBranch });
@@ -344,7 +352,7 @@ public async Task WhenPushToTheRemoteFails_StillCreatesTheBranchLocallyAndAddsIt
     }
 
     [Fact]
-    public async Task WhenV2Schema_AndParentBranchNotProvided_AsksForParentBranch_CreatesNewBranchUnderneathParent()
+    public async Task WhenParentBranchNotProvided_AsksForParentBranch_CreatesNewBranchUnderneathParent()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
@@ -357,7 +365,6 @@ public async Task WhenV2Schema_AndParentBranchNotProvided_AsksForParentBranch_Cr
         var logger = new TestLogger(testOutputHelper);
         var gitClient = Substitute.For<IGitClient>();
         var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V2)
             .WithStack(stack => stack
                 .WithName("Stack1")
                 .WithRemoteUri(remoteUri)
@@ -392,7 +399,7 @@ public async Task WhenV2Schema_AndParentBranchNotProvided_AsksForParentBranch_Cr
     }
 
     [Fact]
-    public async Task WhenV2Schema_AndParentBranchProvided_DoesNotAskForParentBranch_CreatesNewBranchUnderneathParent()
+    public async Task WhenParentBranchProvided_DoesNotAskForParentBranch_CreatesNewBranchUnderneathParent()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
@@ -405,7 +412,6 @@ public async Task WhenV2Schema_AndParentBranchProvided_DoesNotAskForParentBranch
         var logger = new TestLogger(testOutputHelper);
         var gitClient = Substitute.For<IGitClient>();
         var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V2)
             .WithStack(stack => stack
                 .WithName("Stack1")
                 .WithRemoteUri(remoteUri)
@@ -439,43 +445,4 @@ public async Task WhenV2Schema_AndParentBranchProvided_DoesNotAskForParentBranch
 
         inputProvider.DidNotReceive().Select(Questions.SelectParentBranch, Arg.Any<string[]>());
     }
-
-    [Fact]
-    public async Task WhenV1Schema_AndParentBranchProvided_ThrowsException()
-    {
-        // Arrange
-        var sourceBranch = Some.BranchName();
-        var firstBranch = Some.BranchName();
-        var childBranch = Some.BranchName();
-        var newBranch = Some.BranchName();
-        var remoteUri = Some.HttpsUri().ToString();
-
-        var inputProvider = Substitute.For<IInputProvider>();
-        var logger = new TestLogger(testOutputHelper);
-        var gitClient = Substitute.For<IGitClient>();
-        var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V1)
-            .WithStack(stack => stack
-                .WithName("Stack1")
-                .WithRemoteUri(remoteUri)
-                .WithSourceBranch(sourceBranch)
-                .WithBranch(branch => branch.WithName(firstBranch).WithChildBranch(child => child.WithName(childBranch))))
-            .WithStack(stack => stack
-                .WithName("Stack2")
-                .WithRemoteUri(remoteUri)
-                .WithSourceBranch(sourceBranch))
-            .Build();
-        var handler = new NewBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
-
-        inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
-        inputProvider.Text(Questions.BranchName, Arg.Any<string>()).Returns(newBranch);
-        gitClient.GetRemoteUri().Returns(remoteUri);
-        gitClient.GetCurrentBranch().Returns(sourceBranch);
-        gitClient.GetLocalBranchesOrderedByMostRecentCommitterDate().Returns(new[] { sourceBranch, firstBranch, childBranch });
-
-        // Act and assert
-        await handler.Invoking(h => h.Handle(new NewBranchCommandInputs(null, null, firstBranch)))
-            .Should().ThrowAsync<InvalidOperationException>()
-            .WithMessage("Parent branches are not supported in stacks with schema version v1. Please migrate the stack to v2 format.");
-    }
 }
diff --git a/src/Stack.Tests/Commands/Branch/RemoveBranchCommandHandlerTests.cs b/src/Stack.Tests/Commands/Branch/RemoveBranchCommandHandlerTests.cs
index fbf031c0..433a5f11 100644
--- a/src/Stack.Tests/Commands/Branch/RemoveBranchCommandHandlerTests.cs
+++ b/src/Stack.Tests/Commands/Branch/RemoveBranchCommandHandlerTests.cs
@@ -13,7 +13,7 @@ namespace Stack.Tests.Commands.Branch;
 public class RemoveBranchCommandHandlerTests(ITestOutputHelper testOutputHelper)
 {
     [Fact]
-    public async Task WhenNoInputsProvided_AsksForStackAndBranchAndConfirms_RemovesBranchFromStack()
+    public async Task WhenNoInputsProvided_AsksForAllInputsAndConfirms_RemovesBranchFromStack()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
@@ -41,6 +41,8 @@ public async Task WhenNoInputsProvided_AsksForStackAndBranchAndConfirms_RemovesB
 
         inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
         inputProvider.Select(Questions.SelectBranch, Arg.Any<string[]>()).Returns(branchToRemove);
+        inputProvider.Select(Questions.RemoveBranchChildAction, Arg.Any<RemoveBranchChildAction[]>(), Arg.Any<Func<RemoveBranchChildAction, string>>())
+            .Returns(RemoveBranchChildAction.RemoveChildren);
         inputProvider.Confirm(Questions.ConfirmRemoveBranch).Returns(true);
 
         // Act
@@ -291,7 +293,7 @@ public async Task WhenConfirmProvided_DoesNotAskForConfirmation_RemovesBranchFro
     }
 
     [Fact]
-    public async Task WhenSchemaIsV2_AndChildActionIsMoveChildrenToParent_RemovesBranchAndMovesChildrenToParent()
+    public async Task WhenChildActionIsMoveChildrenToParent_RemovesBranchAndMovesChildrenToParent()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
@@ -300,7 +302,6 @@ public async Task WhenSchemaIsV2_AndChildActionIsMoveChildrenToParent_RemovesBra
         var remoteUri = Some.HttpsUri().ToString();
 
         var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V2)
             .WithStack(stack => stack
                 .WithName("Stack1")
                 .WithRemoteUri(remoteUri)
@@ -332,7 +333,7 @@ public async Task WhenSchemaIsV2_AndChildActionIsMoveChildrenToParent_RemovesBra
     }
 
     [Fact]
-    public async Task WhenSchemaIsV2_AndChildActionIsRemoveChildren_RemovesBranchAndDeletesChildren()
+    public async Task WhenChildActionIsRemoveChildren_RemovesBranchAndDeletesChildren()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
@@ -341,7 +342,6 @@ public async Task WhenSchemaIsV2_AndChildActionIsRemoveChildren_RemovesBranchAnd
         var remoteUri = Some.HttpsUri().ToString();
 
         var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V2)
             .WithStack(stack => stack
                 .WithName("Stack1")
                 .WithRemoteUri(remoteUri)
@@ -373,46 +373,7 @@ public async Task WhenSchemaIsV2_AndChildActionIsRemoveChildren_RemovesBranchAnd
     }
 
     [Fact]
-    public async Task WhenSchemaIsV1_RemovesBranchAndMovesChildrenToParent()
-    {
-        // Arrange
-        var sourceBranch = Some.BranchName();
-        var branchToRemove = Some.BranchName();
-        var childBranch = Some.BranchName();
-        var remoteUri = Some.HttpsUri().ToString();
-
-        var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V1)
-            .WithStack(stack => stack
-                .WithName("Stack1")
-                .WithRemoteUri(remoteUri)
-                .WithSourceBranch(sourceBranch)
-                .WithBranch(b => b.WithName(branchToRemove).WithChildBranch(b => b.WithName(childBranch))))
-            .Build();
-        var inputProvider = Substitute.For<IInputProvider>();
-        var logger = new TestLogger(testOutputHelper);
-        var gitClient = Substitute.For<IGitClient>();
-        var handler = new RemoveBranchCommandHandler(inputProvider, logger, gitClient, stackConfig);
-
-        gitClient.GetRemoteUri().Returns(remoteUri);
-        gitClient.GetCurrentBranch().Returns(sourceBranch);
-
-        inputProvider.Select(Questions.SelectStack, Arg.Any<string[]>()).Returns("Stack1");
-        inputProvider.Select(Questions.SelectBranch, Arg.Any<string[]>()).Returns(branchToRemove);
-        inputProvider.Confirm(Questions.ConfirmRemoveBranch).Returns(true);
-
-        // Act
-        await handler.Handle(RemoveBranchCommandInputs.Empty);
-
-        // Assert
-        stackConfig.Stacks.Should().BeEquivalentTo(new List<Config.Stack>
-        {
-            new("Stack1", remoteUri, sourceBranch, [new Config.Branch(childBranch, [])])
-        });
-    }
-
-    [Fact]
-    public async Task WhenSchemaIsV2_AndRemoveChildrenIsProvided_RemovesBranchAndDeletesChildren()
+    public async Task WhenRemoveChildrenIsProvided_RemovesBranchAndDeletesChildren()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
@@ -421,7 +382,6 @@ public async Task WhenSchemaIsV2_AndRemoveChildrenIsProvided_RemovesBranchAndDel
         var remoteUri = Some.HttpsUri().ToString();
 
         var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V2)
             .WithStack(stack => stack
                 .WithName("Stack1")
                 .WithRemoteUri(remoteUri)
@@ -455,7 +415,7 @@ public async Task WhenSchemaIsV2_AndRemoveChildrenIsProvided_RemovesBranchAndDel
     }
 
     [Fact]
-    public async Task WhenSchemaIsV2_AndMoveChildrenToParentIsProvided_RemovesBranchAndMovesChildrenToParent()
+    public async Task WhenMoveChildrenToParentIsProvided_RemovesBranchAndMovesChildrenToParent()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
@@ -464,7 +424,6 @@ public async Task WhenSchemaIsV2_AndMoveChildrenToParentIsProvided_RemovesBranch
         var remoteUri = Some.HttpsUri().ToString();
 
         var stackConfig = new TestStackConfigBuilder()
-            .WithSchemaVersion(SchemaVersion.V2)
             .WithStack(stack => stack
                 .WithName("Stack1")
                 .WithRemoteUri(remoteUri)
diff --git a/src/Stack.Tests/Config/FileStackConfigTests.cs b/src/Stack.Tests/Config/FileStackConfigTests.cs
index c24c7ec3..9ba05b34 100644
--- a/src/Stack.Tests/Config/FileStackConfigTests.cs
+++ b/src/Stack.Tests/Config/FileStackConfigTests.cs
@@ -23,7 +23,7 @@ public void Load_WhenConfigFileDoesNotExist_ReturnsEmptyList()
         var stackData = fileStackConfig.Load();
 
         // Assert
-        stackData.Should().BeEquivalentTo(new StackData(SchemaVersion.V2, []));
+        stackData.Should().BeEquivalentTo(new StackData([]));
     }
 
     [Fact]
@@ -67,7 +67,7 @@ public void Load_WhenConfigFileIsInV1Format_LoadsCorrectly_MigratesAndSavesFileI
         var stackData = fileStackConfig.Load();
 
         // Assert
-        stackData.Should().BeEquivalentTo(new StackData(SchemaVersion.V2, [expectedStack]));
+        stackData.Should().BeEquivalentTo(new StackData([expectedStack]));
         var savedJson = File.ReadAllText(configPath);
         var expectedJson = $@"{{
     ""SchemaVersion"": 2,
@@ -162,62 +162,7 @@ public void Load_WhenConfigFileIsInV2Format_LoadsCorrectly()
         var stackData = fileStackConfig.Load();
 
         // Assert
-        stackData.Should().BeEquivalentTo(new StackData(SchemaVersion.V2, [expectedStack]));
-    }
-
-    [Fact]
-    public void Save_WhenConfigFileIsInV1Format_AndAllStacksHaveASingleTree_SavesCorrectlyInV1Format()
-    {
-        // Arrange
-        using var tempDirectory = TemporaryDirectory.Create();
-        var configPath = Path.Combine(tempDirectory.DirectoryPath, "stack", "config.json");
-        var stackName = Some.Name();
-        var remoteUri = Some.HttpsUri().ToString();
-        var sourceBranch = Some.BranchName();
-        var branch1 = Some.BranchName();
-        var branch2 = Some.BranchName();
-
-        // Create an empty config file
-        Directory.CreateDirectory(Path.GetDirectoryName(configPath)!);
-        File.WriteAllText(configPath, "[]");
-
-        // Create a Stack object with a simple tree structure that should be saved in V1 format
-        var stack = new Config.Stack(
-            stackName,
-            remoteUri,
-            sourceBranch,
-            [
-                new(branch1,
-                    [
-                        new(branch2, [])
-                    ])
-            ]);
-
-        // Act
-        var fileStackConfig = new FileStackConfig(tempDirectory.DirectoryPath);
-        fileStackConfig.Save(new StackData(SchemaVersion.V1, [stack]));
-
-        // Assert
-        var savedJson = File.ReadAllText(configPath);
-
-        // Format the expected JSON string with proper indentation
-        var expectedJson = $@"[
-    {{
-        ""Name"": ""{stackName}"",
-        ""RemoteUri"": ""{remoteUri}"",
-        ""SourceBranch"": ""{sourceBranch}"",
-        ""Branches"": [
-            ""{branch1}"",
-            ""{branch2}""
-        ]
-    }}
-]";
-
-        // Normalize both JSON strings to remove whitespace differences
-        var normalizedSavedJson = NormalizeJsonString(savedJson);
-        var normalizedExpectedJson = NormalizeJsonString(expectedJson);
-
-        normalizedSavedJson.Should().Be(normalizedExpectedJson);
+        stackData.Should().BeEquivalentTo(new StackData([expectedStack]));
     }
 
     [Fact]
@@ -258,7 +203,7 @@ public void Save_WhenConfigFileIsInV1Format_AndStackIsChangedToHaveTreeStructure
         var fileStackConfig = new FileStackConfig(tempDirectory.DirectoryPath);
 
         // Act
-        fileStackConfig.Save(new StackData(SchemaVersion.V2, [stack]));
+        fileStackConfig.Save(new StackData([stack]));
 
         // Assert
         var savedJson = File.ReadAllText(configPath);
diff --git a/src/Stack.Tests/Helpers/TestStackConfigBuilder.cs b/src/Stack.Tests/Helpers/TestStackConfigBuilder.cs
index 29c46f63..dc0d282c 100644
--- a/src/Stack.Tests/Helpers/TestStackConfigBuilder.cs
+++ b/src/Stack.Tests/Helpers/TestStackConfigBuilder.cs
@@ -7,7 +7,6 @@ namespace Stack.Tests.Helpers;
 public class TestStackConfigBuilder
 {
     readonly List<Action<TestStackBuilder>> stackBuilders = [];
-    SchemaVersion schemaVersion = SchemaVersion.V1;
 
     public TestStackConfigBuilder WithStack(Action<TestStackBuilder> stackBuilder)
     {
@@ -15,16 +14,10 @@ public TestStackConfigBuilder WithStack(Action<TestStackBuilder> stackBuilder)
         return this;
     }
 
-    public TestStackConfigBuilder WithSchemaVersion(SchemaVersion version)
-    {
-        schemaVersion = version;
-        return this;
-    }
-
     public TestStackConfig Build()
     {
         return new TestStackConfig(
-            new StackData(schemaVersion, [.. stackBuilders.Select(builder =>
+            new StackData([.. stackBuilders.Select(builder =>
             {
                 var stackBuilder = new TestStackBuilder();
                 builder(stackBuilder);
diff --git a/src/Stack/Commands/Branch/AddBranchCommand.cs b/src/Stack/Commands/Branch/AddBranchCommand.cs
index 1011f437..b0b4803b 100644
--- a/src/Stack/Commands/Branch/AddBranchCommand.cs
+++ b/src/Stack/Commands/Branch/AddBranchCommand.cs
@@ -60,11 +60,6 @@ public override async Task Handle(AddBranchCommandInputs inputs)
             return;
         }
 
-        if (stackData.SchemaVersion == SchemaVersion.V1 && inputs.ParentBranchName is not null)
-        {
-            throw new InvalidOperationException("Parent branches are not supported in stacks with schema version v1. Please migrate the stack to v2 format.");
-        }
-
         var stack = inputProvider.SelectStack(logger, inputs.StackName, stacksForRemote, currentBranch);
 
         if (stack is null)
@@ -86,22 +81,14 @@ public override async Task Handle(AddBranchCommandInputs inputs)
 
         Branch? sourceBranch = null;
 
-        if (stackData.SchemaVersion == SchemaVersion.V1)
-        {
-            // In V1 schema there is only a single set of branches, we always add to the end.
-            sourceBranch = stack.GetAllBranches().LastOrDefault();
-        }
-        if (stackData.SchemaVersion == SchemaVersion.V2)
-        {
-            var parentBranchName = inputProvider.SelectParentBranch(logger, inputs.ParentBranchName, stack);
+        var parentBranchName = inputProvider.SelectParentBranch(logger, inputs.ParentBranchName, stack);
 
-            if (parentBranchName != stack.SourceBranch)
+        if (parentBranchName != stack.SourceBranch)
+        {
+            sourceBranch = stack.GetAllBranches().FirstOrDefault(b => b.Name.Equals(parentBranchName, StringComparison.OrdinalIgnoreCase));
+            if (sourceBranch is null)
             {
-                sourceBranch = stack.GetAllBranches().FirstOrDefault(b => b.Name.Equals(parentBranchName, StringComparison.OrdinalIgnoreCase));
-                if (sourceBranch is null)
-                {
-                    throw new InvalidOperationException($"Branch '{parentBranchName}' not found in stack '{stack.Name}'.");
-                }
+                throw new InvalidOperationException($"Branch '{parentBranchName}' not found in stack '{stack.Name}'.");
             }
         }
 
diff --git a/src/Stack/Commands/Branch/NewBranchCommand.cs b/src/Stack/Commands/Branch/NewBranchCommand.cs
index 4be3957d..505bf0c1 100644
--- a/src/Stack/Commands/Branch/NewBranchCommand.cs
+++ b/src/Stack/Commands/Branch/NewBranchCommand.cs
@@ -62,11 +62,6 @@ public override async Task Handle(NewBranchCommandInputs inputs)
             return;
         }
 
-        if (stackData.SchemaVersion == SchemaVersion.V1 && inputs.ParentBranchName is not null)
-        {
-            throw new InvalidOperationException("Parent branches are not supported in stacks with schema version v1. Please migrate the stack to v2 format.");
-        }
-
         var stack = inputProvider.SelectStack(logger, inputs.StackName, stacksForRemote, currentBranch);
 
         if (stack is null)
@@ -88,22 +83,14 @@ public override async Task Handle(NewBranchCommandInputs inputs)
 
         Branch? sourceBranch = null;
 
-        if (stackData.SchemaVersion == SchemaVersion.V1)
-        {
-            // In V1 schema there is only a single set of branches, we always add to the end.
-            sourceBranch = stack.GetAllBranches().LastOrDefault();
-        }
-        if (stackData.SchemaVersion == SchemaVersion.V2)
-        {
-            var parentBranchName = inputProvider.SelectParentBranch(logger, inputs.ParentBranchName, stack);
+        var parentBranchName = inputProvider.SelectParentBranch(logger, inputs.ParentBranchName, stack);
 
-            if (parentBranchName != stack.SourceBranch)
+        if (parentBranchName != stack.SourceBranch)
+        {
+            sourceBranch = stack.GetAllBranches().FirstOrDefault(b => b.Name.Equals(parentBranchName, StringComparison.OrdinalIgnoreCase));
+            if (sourceBranch is null)
             {
-                sourceBranch = stack.GetAllBranches().FirstOrDefault(b => b.Name.Equals(parentBranchName, StringComparison.OrdinalIgnoreCase));
-                if (sourceBranch is null)
-                {
-                    throw new InvalidOperationException($"Branch '{parentBranchName}' not found in stack '{stack.Name}'.");
-                }
+                throw new InvalidOperationException($"Branch '{parentBranchName}' not found in stack '{stack.Name}'.");
             }
         }
 
diff --git a/src/Stack/Commands/Branch/RemoveBranchCommand.cs b/src/Stack/Commands/Branch/RemoveBranchCommand.cs
index 3430e24d..1ccbdaa7 100644
--- a/src/Stack/Commands/Branch/RemoveBranchCommand.cs
+++ b/src/Stack/Commands/Branch/RemoveBranchCommand.cs
@@ -87,17 +87,12 @@ public override async Task Handle(RemoveBranchCommandInputs inputs)
             throw new InvalidOperationException($"Branch '{branchName}' not found in stack '{stack.Name}'.");
         }
 
-        var action = RemoveBranchChildAction.MoveChildrenToParent;
-
-        if (stackData.SchemaVersion == SchemaVersion.V2)
-        {
-            action =
-                inputs.RemoveChildrenAction ??
-                inputProvider.Select(
-                    Questions.RemoveBranchChildAction,
-                    [RemoveBranchChildAction.MoveChildrenToParent, RemoveBranchChildAction.RemoveChildren],
-                    (action) => action.Humanize());
-        }
+        var action =
+            inputs.RemoveChildrenAction ??
+            inputProvider.Select(
+                Questions.RemoveBranchChildAction,
+                [RemoveBranchChildAction.MoveChildrenToParent, RemoveBranchChildAction.RemoveChildren],
+                (action) => action.Humanize());
 
         if (inputs.Confirm || inputProvider.Confirm(Questions.ConfirmRemoveBranch))
         {
diff --git a/src/Stack/Commands/Helpers/StackHelpers.cs b/src/Stack/Commands/Helpers/StackHelpers.cs
index d7fcb1f8..40ddae85 100644
--- a/src/Stack/Commands/Helpers/StackHelpers.cs
+++ b/src/Stack/Commands/Helpers/StackHelpers.cs
@@ -239,19 +239,17 @@ public static StackStatus GetStackStatus(
     }
 
     public static void OutputStackStatus(
-        SchemaVersion schemaVersion,
         List<StackStatus> statuses,
         ILogger logger)
     {
         foreach (var status in statuses)
         {
-            OutputStackStatus(schemaVersion, status, logger);
+            OutputStackStatus(status, logger);
             logger.NewLine();
         }
     }
 
     public static void OutputStackStatus(
-        SchemaVersion schemaVersion,
         StackStatus status,
         ILogger logger,
         Func<BranchDetail, string?>? getBranchPullRequestDisplay = null)
@@ -264,11 +262,6 @@ public static void OutputStackStatus(
             items.Add(GetBranchAndPullRequestStatusOutput(branch, getBranchPullRequestDisplay));
         }
 
-        if (schemaVersion == SchemaVersion.V1 && items.Count > 0)
-        {
-            items = [.. MoreEnumerable.TraverseDepthFirst(items.First(), i => i.Children).Select(i => new TreeItem<string>(i.Value, []))];
-        }
-
         logger.Information(status.Name.Stack());
         logger.Tree(new Tree<string>(header, [.. items]));
     }
diff --git a/src/Stack/Commands/PullRequests/CreatePullRequestsCommand.cs b/src/Stack/Commands/PullRequests/CreatePullRequestsCommand.cs
index 545e229d..ff76b9e7 100644
--- a/src/Stack/Commands/PullRequests/CreatePullRequestsCommand.cs
+++ b/src/Stack/Commands/PullRequests/CreatePullRequestsCommand.cs
@@ -97,7 +97,7 @@ public override async Task Handle(CreatePullRequestsCommandInputs inputs)
             }
         }
 
-        StackHelpers.OutputStackStatus(stackData.SchemaVersion, status, logger);
+        StackHelpers.OutputStackStatus(status, logger);
 
         logger.NewLine();
 
@@ -128,7 +128,7 @@ public override async Task Handle(CreatePullRequestsCommandInputs inputs)
 
             logger.NewLine();
 
-            OutputUpdatedStackStatus(logger, stackData.SchemaVersion, stack, status, pullRequestInformation);
+            OutputUpdatedStackStatus(logger, stack, status, pullRequestInformation);
 
             logger.NewLine();
 
@@ -191,13 +191,11 @@ private static List<GitHubPullRequest> CreatePullRequests(
 
     private static void OutputUpdatedStackStatus(
         ILogger logger,
-        SchemaVersion schemaVersion,
         Config.Stack stack,
         StackStatus status,
         List<PullRequestInformation> pullRequestInformation)
     {
         StackHelpers.OutputStackStatus(
-            schemaVersion,
             status,
             logger,
             (branch) =>
diff --git a/src/Stack/Commands/Remote/SyncStackCommand.cs b/src/Stack/Commands/Remote/SyncStackCommand.cs
index 451acc83..cf4fc4df 100644
--- a/src/Stack/Commands/Remote/SyncStackCommand.cs
+++ b/src/Stack/Commands/Remote/SyncStackCommand.cs
@@ -101,7 +101,7 @@ public override async Task Handle(SyncStackCommandInputs inputs)
             gitHubClient,
             true);
 
-        StackHelpers.OutputStackStatus(stackData.SchemaVersion, status, logger);
+        StackHelpers.OutputStackStatus(status, logger);
 
         logger.NewLine();
 
diff --git a/src/Stack/Commands/Stack/StackStatusCommand.cs b/src/Stack/Commands/Stack/StackStatusCommand.cs
index d62ed471..5aa449d6 100644
--- a/src/Stack/Commands/Stack/StackStatusCommand.cs
+++ b/src/Stack/Commands/Stack/StackStatusCommand.cs
@@ -115,7 +115,7 @@ protected override async Task<StackStatusCommandResponse> ExecuteAndReturnRespon
 
     protected override void WriteDefaultOutput(StackStatusCommandResponse response)
     {
-        StackHelpers.OutputStackStatus(response.SchemaVersion, response.Stacks, StdOutLogger);
+        StackHelpers.OutputStackStatus(response.Stacks, StdOutLogger);
 
         if (response.Stacks.Count == 1)
         {
@@ -188,7 +188,7 @@ private static StackStatusCommandJsonOutputBranchDetail MapBranchDetail(BranchDe
 }
 
 public record StackStatusCommandInputs(string? Stack, bool All, bool Full);
-public record StackStatusCommandResponse(SchemaVersion SchemaVersion, List<StackStatus> Stacks);
+public record StackStatusCommandResponse(List<StackStatus> Stacks);
 
 public class StackStatusCommandHandler(
     IInputProvider inputProvider,
@@ -233,6 +233,6 @@ public override async Task<StackStatusCommandResponse> Handle(StackStatusCommand
             gitHubClient,
             inputs.Full);
 
-        return new StackStatusCommandResponse(stackData.SchemaVersion, stackStatusResults);
+        return new StackStatusCommandResponse(stackStatusResults);
     }
 }
\ No newline at end of file
diff --git a/src/Stack/Config/StackConfig.cs b/src/Stack/Config/StackConfig.cs
index cd1801dc..3795479f 100644
--- a/src/Stack/Config/StackConfig.cs
+++ b/src/Stack/Config/StackConfig.cs
@@ -3,7 +3,7 @@
 
 namespace Stack.Config;
 
-public record StackData(SchemaVersion SchemaVersion, List<Stack> Stacks);
+public record StackData(List<Stack> Stacks);
 
 public interface IStackConfig
 {
@@ -35,18 +35,18 @@ public StackData Load()
         var stacksFile = GetConfigPath();
         if (!File.Exists(stacksFile))
         {
-            return new StackData(SchemaVersion.V2, []);
+            return new StackData([]);
         }
         var jsonString = File.ReadAllText(stacksFile);
 
         if (IsStackConfigInV2Format(jsonString))
         {
-            return new StackData(SchemaVersion.V2, LoadStacksFromV2Format(jsonString));
+            return new StackData(LoadStacksFromV2Format(jsonString));
         }
 
         // If no schema version, this means v1 format - migrate to v2 format and re-save before returning
         var stacksV1 = LoadStacksFromV1Format(jsonString);
-        var stacks = new StackData(SchemaVersion.V2, stacksV1);
+        var stacks = new StackData(stacksV1);
         Save(stacks);
         return stacks;
     }
@@ -59,19 +59,7 @@ public void Save(StackData stackData)
             Directory.CreateDirectory(Path.GetDirectoryName(stacksFile)!);
         }
 
-        if (stackData.SchemaVersion == SchemaVersion.V1)
-        {
-            if (stackData.Stacks.Any(s => !s.HasSingleTree))
-            {
-                throw new InvalidOperationException("Cannot save in v1 format if any stack has multiple trees.");
-            }
-
-            // If all stacks have a single tree and we are still in v1 format continue to preference this.
-            File.WriteAllText(stacksFile, JsonSerializer.Serialize(stackData.Stacks.Select(MapToV1Format).ToList(), StackConfigJsonSerializerContext.Default.ListStackV1));
-            return;
-        }
-
-        // Else we are writing in v2 format
+        // We only write in v2 format
         var existingConfigFileIsInV1Format = false;
 
         if (File.Exists(stacksFile))