diff --git a/README.md b/README.md
index 36802432..60690443 100644
--- a/README.md
+++ b/README.md
@@ -136,9 +136,13 @@ To use the rebase strategy, either:
 
 To push changes to the remote after rebasing you'll need to use the `--force-with-lease` option.
 
-**Rough edges**
+**_Squash merges_**
+
+A common pattern when using pull requests is to Squash Merge the pull request when merging into the target branch, squashing all the commits in the PR branch into a single commit. This causes issues when rebasing the rest of the child branches in the stack.
+
+Stack has handling to detect when a squash merge happens during updating a stack using rebase as the update strategy. It will skip the commits that were squash merged, avoiding conflicts.
 
-If you merge a pull request using "Squash and merge" then you might find that the first update to a stack after that results in merge conflicts that you need to resolve. This can be a bit of a pain, however for each commit that existed on the branch that was merged if you select to take the new single commit that now exists generally it isn't too bad.
+The remote tracking branch for the branch that was squash merged needs to be deleted for this handling to be enabled.
 
 ### Creating pull requests
 
diff --git a/src/Stack.Tests/Commands/Helpers/StackActionsTests.cs b/src/Stack.Tests/Commands/Helpers/StackActionsTests.cs
index faedcead..ba9a5e0c 100644
--- a/src/Stack.Tests/Commands/Helpers/StackActionsTests.cs
+++ b/src/Stack.Tests/Commands/Helpers/StackActionsTests.cs
@@ -12,16 +12,17 @@ namespace Stack.Tests.Helpers;
 public class StackActionsTests(ITestOutputHelper testOutputHelper)
 {
     [Fact]
-    public async Task UpdateStack_UsingMerge_WhenConflictAbortedBeforeProgressRecorded_ThrowsAbortException()
+    public async Task UpdateStack_UsingMerge_WhenConflictResolutionAborted_ThrowsAbortException()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
         var feature = Some.BranchName();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
         var stack = new Config.Stack("Stack1", Some.HttpsUri().ToString(), sourceBranch, new List<Config.Branch> { new(feature, []) });
 
         gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
@@ -32,15 +33,14 @@ public async Task UpdateStack_UsingMerge_WhenConflictAbortedBeforeProgressRecord
 
         // Trigger conflict
         gitClient.When(g => g.MergeFromLocalSourceBranch(sourceBranch)).Throws(new ConflictException());
-        // Simulate: initial check says merge in progress, then still in progress once, then not in progress with HEAD unchanged => aborted
-        gitClient.IsMergeInProgress().Returns(true, true, false);
+        conflictResolutionDetector
+            .WaitForConflictResolution(gitClient, logger, ConflictOperationType.Merge, Arg.Any<TimeSpan>(), Arg.Any<TimeSpan?>(), Arg.Any<CancellationToken>())
+            .Returns(ConflictResolutionResult.Aborted);
 
-        var head = Some.Sha();
-        gitClient.GetHeadSha().Returns(head, head, head); // unchanged
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var actions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var actions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         var act = async () => await actions.UpdateStack(stack, UpdateStrategy.Merge, CancellationToken.None);
@@ -50,16 +50,17 @@ public async Task UpdateStack_UsingMerge_WhenConflictAbortedBeforeProgressRecord
     }
 
     [Fact]
-    public async Task UpdateStack_UsingMerge_WhenConflictResolved_CompletesSuccessfully()
+    public async Task UpdateStack_UsingMerge_WhenConflictsResolved_CompletesSuccessfully()
     {
         // Arrange
         var sourceBranch = Some.BranchName();
         var feature = Some.BranchName();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
         var stack = new Config.Stack("Stack1", Some.HttpsUri().ToString(), sourceBranch, new List<Config.Branch> { new(feature, []) });
 
         gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
@@ -70,13 +71,13 @@ public async Task UpdateStack_UsingMerge_WhenConflictResolved_CompletesSuccessfu
 
         gitClient.When(g => g.MergeFromLocalSourceBranch(sourceBranch)).Throws(new ConflictException());
 
-        // Merge progress -> then resolved (not in progress) with different HEAD
-        gitClient.IsMergeInProgress().Returns(true, false);
-        gitClient.GetHeadSha().Returns(Some.Sha(), Some.Sha()); // changed
+        conflictResolutionDetector
+            .WaitForConflictResolution(gitClient, logger, ConflictOperationType.Merge, Arg.Any<TimeSpan>(), Arg.Any<TimeSpan?>(), Arg.Any<CancellationToken>())
+            .Returns(ConflictResolutionResult.Completed);
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var actions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var actions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         await actions.UpdateStack(stack, UpdateStrategy.Merge, CancellationToken.None);
@@ -86,16 +87,17 @@ public async Task UpdateStack_UsingMerge_WhenConflictResolved_CompletesSuccessfu
     }
 
     [Fact]
-    public async Task UpdateStack_UsingRebase_WhenConflictAbortedBeforeProgressRecorded_ThrowsAbortException()
+    public async Task UpdateStack_UsingRebase_WhenConflictResolutionAborted_ThrowsAbortException()
     {
         // Arrange
         var source = Some.BranchName();
         var feature = Some.BranchName();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
         var stack = new Config.Stack("Stack1", Some.HttpsUri().ToString(), source, new List<Config.Branch> { new(feature, []) });
 
         gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
@@ -105,16 +107,14 @@ public async Task UpdateStack_UsingRebase_WhenConflictAbortedBeforeProgressRecor
         });
 
         gitClient.When(g => g.RebaseFromLocalSourceBranch(source)).Throws(new ConflictException());
-        gitClient.IsRebaseInProgress().Returns(true, true, false);
-        var origHead = Some.Sha();
+        conflictResolutionDetector
+            .WaitForConflictResolution(gitClient, logger, ConflictOperationType.Rebase, Arg.Any<TimeSpan>(), Arg.Any<TimeSpan?>(), Arg.Any<CancellationToken>())
+            .Returns(ConflictResolutionResult.Aborted);
 
-        // During rebase conflict HEAD may move; ensure orig head stored and final head equals orig to simulate abort
-        gitClient.GetOriginalHeadSha().Returns(origHead);
-        gitClient.GetHeadSha().Returns(origHead, origHead, origHead);
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var actions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var actions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         var act = async () => await actions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
@@ -124,16 +124,17 @@ public async Task UpdateStack_UsingRebase_WhenConflictAbortedBeforeProgressRecor
     }
 
     [Fact]
-    public async Task UpdateStack_UsingRebase_WhenConflictResolved_CompletesSuccessfully()
+    public async Task UpdateStack_UsingRebase_WhenConflictsResolved_CompletesSuccessfully()
     {
         // Arrange
         var source = Some.BranchName();
         var feature = Some.BranchName();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
         var stack = new Config.Stack("Stack1", Some.HttpsUri().ToString(), source, new List<Config.Branch> { new(feature, []) });
 
         gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
@@ -143,17 +144,14 @@ public async Task UpdateStack_UsingRebase_WhenConflictResolved_CompletesSuccessf
         });
 
         gitClient.When(g => g.RebaseFromLocalSourceBranch(source)).Throws(new ConflictException());
-        gitClient.IsRebaseInProgress().Returns(true, false);
-
-        var origHead = Some.Sha();
-        var newHead = Some.Sha();
-        gitClient.GetOriginalHeadSha().Returns(origHead);
-        gitClient.GetHeadSha().Returns(newHead, newHead); // changed from original
+        conflictResolutionDetector
+            .WaitForConflictResolution(gitClient, logger, ConflictOperationType.Rebase, Arg.Any<TimeSpan>(), Arg.Any<TimeSpan?>(), Arg.Any<CancellationToken>())
+            .Returns(ConflictResolutionResult.Completed);
 
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var actions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var actions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         await actions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
@@ -162,232 +160,6 @@ public async Task UpdateStack_UsingRebase_WhenConflictResolved_CompletesSuccessf
         gitClient.Received().ChangeBranch(feature);
     }
 
-    [Fact]
-    public async Task UpdateStack_UsingRebase_WhenARemoteBranchIsDeleted_RebasesOntoTheParentBranchToAvoidConflicts()
-    {
-        // Arrange
-        var sourceBranch = Some.BranchName();
-        var branch1 = Some.BranchName();
-        var branch2 = Some.BranchName();
-        var gitClient = Substitute.For<IGitClient>();
-        var gitHubClient = Substitute.For<IGitHubClient>();
-        var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
-
-        // Setup branch statuses to simulate the scenario
-        gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
-        {
-            { sourceBranch, new GitBranchStatus(sourceBranch, $"origin/{sourceBranch}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch1, new GitBranchStatus(branch1, $"origin/{branch1}", false, false, 0, 0, new Commit(Some.Sha(), Some.Name())) }, // remote branch deleted
-            { branch2, new GitBranchStatus(branch2, $"origin/{branch2}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) }
-        });
-        gitClient.IsAncestor(branch2, branch1).Returns(true);
-
-        var stack = new Config.Stack(
-            "Stack1",
-            Some.HttpsUri().ToString(),
-            sourceBranch,
-            new List<Config.Branch> { new Config.Branch(branch1, new List<Config.Branch> { new Config.Branch(branch2, new List<Config.Branch>()) }) }
-        );
-
-        var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
-        var factory = Substitute.For<IGitClientFactory>();
-        factory.Create(executionContext.WorkingDirectory).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
-
-        // Act
-        await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
-
-        // Assert
-        gitClient.Received().ChangeBranch(branch2);
-        gitClient.Received().RebaseOntoNewParent(sourceBranch, branch1);
-    }
-
-    [Fact]
-    public async Task UpdateStack_UsingRebase_WhenARemoteBranchIsDeleted_ButTheTargetBranchHasAlreadyHadAdditionalCommitsMergedInto_DoesNotRebaseOntoTheParentBranch()
-    {
-        // Arrange
-        var sourceBranch = Some.BranchName();
-        var branch1 = Some.BranchName();
-        var branch2 = Some.BranchName();
-        var changedFilePath = Some.Name();
-
-        var gitClient = Substitute.For<IGitClient>();
-        var gitHubClient = Substitute.For<IGitHubClient>();
-        var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
-
-        // Setup branch statuses to simulate the scenario
-        gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
-        {
-            { sourceBranch, new GitBranchStatus(sourceBranch, $"origin/{sourceBranch}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch1, new GitBranchStatus(branch1, $"origin/{branch1}", false, false, 0, 0, new Commit(Some.Sha(), Some.Name())) }, // remote branch deleted
-            { branch2, new GitBranchStatus(branch2, $"origin/{branch2}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) }
-        });
-        gitClient.IsAncestor(branch2, branch1).Returns(false);
-
-        var stack = new Config.Stack(
-            "Stack1",
-            Some.HttpsUri().ToString(),
-            sourceBranch,
-            new List<Config.Branch> { new Config.Branch(branch1, new List<Config.Branch> { new Config.Branch(branch2, new List<Config.Branch>()) }) }
-        );
-
-        var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
-        var factory = Substitute.For<IGitClientFactory>();
-        factory.Create(executionContext.WorkingDirectory).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
-
-        // Act
-        await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
-
-        // Assert
-        gitClient.Received().ChangeBranch(branch2);
-        gitClient.Received().RebaseFromLocalSourceBranch(sourceBranch);
-    }
-
-    [Fact]
-    public async Task UpdateStack_UsingRebase_WhenARemoteBranchIsDeleted_AndLocalBranchIsDeleted_DoesNotRebaseOntoTheParentBranch()
-    {
-        // Arrange
-        var sourceBranch = Some.BranchName();
-        var branch1 = Some.BranchName();
-        var branch2 = Some.BranchName();
-        var gitClient = Substitute.For<IGitClient>();
-        var gitHubClient = Substitute.For<IGitHubClient>();
-        var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-
-        gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
-        {
-            { sourceBranch, new GitBranchStatus(sourceBranch, $"origin/{sourceBranch}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch1, new GitBranchStatus(branch1, $"origin/{branch1}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch2, new GitBranchStatus(branch2, $"origin/{branch2}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) }
-        });
-
-        var stack = new Config.Stack(
-            "Stack1",
-            Some.HttpsUri().ToString(),
-            sourceBranch,
-            new List<Config.Branch> { new Config.Branch(branch1, new List<Config.Branch> { new Config.Branch(branch2, new List<Config.Branch>()) }) }
-        );
-
-        var console = new TestDisplayProvider(testOutputHelper);
-        var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
-        var factory = Substitute.For<IGitClientFactory>();
-        factory.Create(executionContext.WorkingDirectory).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
-
-        gitClient.Fetch(true);
-
-        // Act
-        await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
-
-        // Assert
-        gitClient.Received().ChangeBranch(branch2);
-    }
-
-    [Fact]
-    public async Task UpdateStack_UsingRebase_WhenStackHasATreeStructure_RebasesAllBranchesCorrectly()
-    {
-        // Arrange
-        var sourceBranch = "source-branch";
-        var branch1 = "branch-1";
-        var branch2 = "branch-2";
-        var branch3 = "branch-3";
-
-        var gitClient = Substitute.For<IGitClient>();
-        var gitHubClient = Substitute.For<IGitHubClient>();
-        var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
-
-        gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
-        {
-            { sourceBranch, new GitBranchStatus(sourceBranch, $"origin/{sourceBranch}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch1, new GitBranchStatus(branch1, $"origin/{branch1}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch2, new GitBranchStatus(branch2, $"origin/{branch2}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch3, new GitBranchStatus(branch3, $"origin/{branch3}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) }
-        });
-
-        var stack = new Config.Stack(
-            "Stack1",
-            Some.HttpsUri().ToString(),
-            sourceBranch,
-            new List<Config.Branch> { new Config.Branch(branch1, new List<Config.Branch> { new Config.Branch(branch2, new List<Config.Branch>()), new Config.Branch(branch3, new List<Config.Branch>()) }) }
-        );
-
-        var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
-        var factory = Substitute.For<IGitClientFactory>();
-        factory.Create(executionContext.WorkingDirectory).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
-
-        // Act
-        await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
-
-        // Assert
-        Received.InOrder(() =>
-        {
-            gitClient.ChangeBranch(branch2);
-            gitClient.RebaseFromLocalSourceBranch(branch1);
-            gitClient.ChangeBranch(branch2);
-            gitClient.RebaseFromLocalSourceBranch(sourceBranch);
-            gitClient.ChangeBranch(branch3);
-            gitClient.RebaseFromLocalSourceBranch(branch1);
-            gitClient.ChangeBranch(branch3);
-            gitClient.RebaseFromLocalSourceBranch(sourceBranch);
-        });
-    }
-
-    [Fact]
-    public async Task UpdateStack_UsingMerge_WhenStackHasATreeStructure_MergesAllBranchesCorrectly()
-    {
-        // Arrange
-        var sourceBranch = "source-branch";
-        var branch1 = "branch-1";
-        var branch2 = "branch-2";
-        var branch3 = "branch-3";
-
-        var gitClient = Substitute.For<IGitClient>();
-        var gitHubClient = Substitute.For<IGitHubClient>();
-        var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
-
-        gitClient.GetBranchStatuses(Arg.Any<string[]>()).Returns(new Dictionary<string, GitBranchStatus>
-        {
-            { sourceBranch, new GitBranchStatus(sourceBranch, $"origin/{sourceBranch}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch1, new GitBranchStatus(branch1, $"origin/{branch1}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch2, new GitBranchStatus(branch2, $"origin/{branch2}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) },
-            { branch3, new GitBranchStatus(branch3, $"origin/{branch3}", true, false, 0, 0, new Commit(Some.Sha(), Some.Name())) }
-        });
-
-        var stack = new Config.Stack(
-            "Stack1",
-            Some.HttpsUri().ToString(),
-            sourceBranch,
-            new List<Config.Branch> { new Config.Branch(branch1, new List<Config.Branch> { new Config.Branch(branch2, new List<Config.Branch>()), new Config.Branch(branch3, new List<Config.Branch>()) }) }
-        );
-
-        var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
-        var factory = Substitute.For<IGitClientFactory>();
-        factory.Create(executionContext.WorkingDirectory).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
-
-        // Act
-        await stackActions.UpdateStack(stack, UpdateStrategy.Merge, CancellationToken.None);
-
-        // Assert that merges were attempted
-        Received.InOrder(() =>
-        {
-            gitClient.ChangeBranch(branch1);
-            gitClient.MergeFromLocalSourceBranch(sourceBranch);
-            gitClient.ChangeBranch(branch2);
-            gitClient.MergeFromLocalSourceBranch(branch1);
-            gitClient.ChangeBranch(branch1);
-            gitClient.MergeFromLocalSourceBranch(sourceBranch);
-            gitClient.ChangeBranch(branch3);
-            gitClient.MergeFromLocalSourceBranch(branch1);
-        });
-    }
-
     [Fact]
     public void PullChanges_WhenSomeBranchesHaveChanges_AndOthersDoNot_OnlyPullsChangesForBranchesThatNeedIt()
     {
@@ -399,7 +171,8 @@ public void PullChanges_WhenSomeBranchesHaveChanges_AndOthersDoNot_OnlyPullsChan
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var branchStatus = new Dictionary<string, GitBranchStatus>
         {
@@ -419,7 +192,7 @@ public void PullChanges_WhenSomeBranchesHaveChanges_AndOthersDoNot_OnlyPullsChan
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(executionContext.WorkingDirectory).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -440,7 +213,8 @@ public void PullChanges_WhenSomeBranchesDoNotExistInRemote_OnlyPullsBranchesThat
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var branchStatus = new Dictionary<string, GitBranchStatus>
         {
@@ -460,7 +234,7 @@ public void PullChanges_WhenSomeBranchesDoNotExistInRemote_OnlyPullsBranchesThat
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(executionContext.WorkingDirectory).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -482,7 +256,8 @@ public void PullChanges_WhenOnlyNonCurrentBranchesBehind_FetchesThem()
         var gitHubClient = Substitute.For<IGitHubClient>();
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var statuses = new Dictionary<string, GitBranchStatus>
         {
@@ -504,7 +279,7 @@ public void PullChanges_WhenOnlyNonCurrentBranchesBehind_FetchesThem()
         var worktreePath = "/worktree";
         factory.Create(executionContext.WorkingDirectory).Returns(gitClient);
         factory.Create(worktreePath).Returns(worktreeGitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -523,7 +298,8 @@ public void PullChanges_WhenOnlyCurrentBranchBehind_PullsIt()
         var gitHubClient = Substitute.For<IGitHubClient>();
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var statuses = new Dictionary<string, GitBranchStatus>
         {
@@ -536,7 +312,7 @@ public void PullChanges_WhenOnlyCurrentBranchBehind_PullsIt()
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -555,7 +331,8 @@ public void PullChanges_WhenCurrentAndOtherBranchesBehind_PullsCurrentAndFetches
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         var statuses = new Dictionary<string, GitBranchStatus>
@@ -573,7 +350,7 @@ public void PullChanges_WhenCurrentAndOtherBranchesBehind_PullsCurrentAndFetches
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -592,7 +369,8 @@ public void PullChanges_WhenNoBranchesBehind_DoesNothing()
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         var statuses = new Dictionary<string, GitBranchStatus>
@@ -606,7 +384,7 @@ public void PullChanges_WhenNoBranchesBehind_DoesNothing()
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -628,7 +406,8 @@ public void PullChanges_WhenBranchIsBehind_AndCheckedOutInAnotherWorktree_PullsI
         var worktreeGitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         defaultGitClient.GetCurrentBranch().Returns(sourceBranch);
         var statuses = new Dictionary<string, GitBranchStatus>
@@ -648,7 +427,7 @@ public void PullChanges_WhenBranchIsBehind_AndCheckedOutInAnotherWorktree_PullsI
         factory.Create(executionContext.WorkingDirectory).Returns(defaultGitClient);
         factory.Create(worktreePath).Returns(worktreeGitClient);
 
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -669,7 +448,8 @@ public void PushChanges_WhenSomeLocalBranchesAreAhead_OnlyPushesChangesForBranch
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var branchStatus = new Dictionary<string, GitBranchStatus>
         {
@@ -695,7 +475,7 @@ public void PushChanges_WhenSomeLocalBranchesAreAhead_OnlyPushesChangesForBranch
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, 5, false);
@@ -715,7 +495,8 @@ public void PushChanges_WhenSomeBranchesDoNotExistInRemote_OnlyPushesBranchesTha
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var branchStatus = new Dictionary<string, GitBranchStatus>
         {
@@ -741,7 +522,7 @@ public void PushChanges_WhenSomeBranchesDoNotExistInRemote_OnlyPushesBranchesTha
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, 5, false);
@@ -761,7 +542,8 @@ public void PushChanges_WhenSomeBranchesHaveNoRemoteTrackingBranch_PushesThemAsN
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var branchStatus = new Dictionary<string, GitBranchStatus>
         {
@@ -792,7 +574,7 @@ public void PushChanges_WhenSomeBranchesHaveNoRemoteTrackingBranch_PushesThemAsN
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, 5, false);
@@ -814,7 +596,8 @@ public void PushChanges_WhenMaxBatchSizeIsSmaller_PushesBranchesInMultipleBatche
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var branchStatus = new Dictionary<string, GitBranchStatus>
         {
@@ -842,7 +625,7 @@ public void PushChanges_WhenMaxBatchSizeIsSmaller_PushesBranchesInMultipleBatche
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, maxBatchSize: 2, forceWithLease: false);
@@ -864,7 +647,8 @@ public void PushChanges_WhenForceWithLeaseIsTrue_PassesForceWithLeaseParameterTo
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var branchStatus = new Dictionary<string, GitBranchStatus>
         {
@@ -882,7 +666,7 @@ public void PushChanges_WhenForceWithLeaseIsTrue_PassesForceWithLeaseParameterTo
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, maxBatchSize: 5, forceWithLease: true);
@@ -902,7 +686,8 @@ public void PushChanges_WhenNoBranchesNeedToBePushed_DoesNotCallPushMethods()
         var gitClient = Substitute.For<IGitClient>();
         var gitHubClient = Substitute.For<IGitHubClient>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         var branchStatus = new Dictionary<string, GitBranchStatus>
         {
@@ -922,7 +707,7 @@ public void PushChanges_WhenNoBranchesNeedToBePushed_DoesNotCallPushMethods()
         var executionContext = new CliExecutionContext { WorkingDirectory = "/repo" };
         var factory = Substitute.For<IGitClientFactory>();
         factory.Create(Arg.Any<string>()).Returns(gitClient);
-        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(factory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, maxBatchSize: 5, forceWithLease: false);
@@ -944,9 +729,10 @@ public async Task UpdateStack_UsingMerge_WhenBranchIsInWorktree_UsesWorktreeGitC
         var gitHubClient = Substitute.For<IGitHubClient>();
         var inputProvider = Substitute.For<IInputProvider>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
         var gitClientFactory = Substitute.For<IGitClientFactory>();
         var worktreeGitClient = Substitute.For<IGitClient>();
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         gitClientFactory.Create(worktreePath).Returns(worktreeGitClient);
@@ -966,7 +752,7 @@ public async Task UpdateStack_UsingMerge_WhenBranchIsInWorktree_UsesWorktreeGitC
         );
 
         var executionContext = new CliExecutionContext { WorkingDirectory = "/some/path" };
-        var stackActions = new StackActions(gitClientFactory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(gitClientFactory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         gitClientFactory.Create(executionContext.WorkingDirectory).Returns(gitClient);
 
@@ -991,9 +777,10 @@ public async Task UpdateStack_UsingRebase_WhenBranchIsInWorktree_UsesWorktreeGit
         var gitHubClient = Substitute.For<IGitHubClient>();
         var inputProvider = Substitute.For<IInputProvider>();
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var console = new TestDisplayProvider(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
         var gitClientFactory = Substitute.For<IGitClientFactory>();
         var worktreeGitClient = Substitute.For<IGitClient>();
+        var conflictResolutionDetector = Substitute.For<IConflictResolutionDetector>();
 
         gitClient.GetCurrentBranch().Returns(sourceBranch);
         gitClientFactory.Create(worktreePath).Returns(worktreeGitClient);
@@ -1013,7 +800,7 @@ public async Task UpdateStack_UsingRebase_WhenBranchIsInWorktree_UsesWorktreeGit
         );
 
         var executionContext = new CliExecutionContext { WorkingDirectory = "/some/path" };
-        var stackActions = new StackActions(gitClientFactory, executionContext, gitHubClient, logger, console);
+        var stackActions = new StackActions(gitClientFactory, executionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         gitClientFactory.Create(executionContext.WorkingDirectory).Returns(gitClient);
 
diff --git a/src/Stack.Tests/Git/ConflictResolutionDetectorTests.cs b/src/Stack.Tests/Git/ConflictResolutionDetectorTests.cs
index 0bfd6427..4bfaa843 100644
--- a/src/Stack.Tests/Git/ConflictResolutionDetectorTests.cs
+++ b/src/Stack.Tests/Git/ConflictResolutionDetectorTests.cs
@@ -40,7 +40,9 @@ public async Task WaitForConflictResolution_WhenNotStarted_ReturnsNotStarted()
         var logger = CreateLogger<ConflictResolutionDetectorTests>();
         var git = new GitClient(XUnitLogger.CreateLogger<GitClient>(testOutputHelper), repo.LocalDirectoryPath);
 
-        var result = await ConflictResolutionDetector.WaitForConflictResolution(
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
+        var result = await conflictResolutionDetector.WaitForConflictResolution(
             git,
             logger,
             ConflictOperationType.Merge,
@@ -64,6 +66,8 @@ public async Task WaitForConflictResolution_WhenMergeCompletes_ReturnsCompleted(
         var logger = CreateLogger<ConflictResolutionDetectorTests>();
         var git = new GitClient(XUnitLogger.CreateLogger<GitClient>(testOutputHelper), repo.LocalDirectoryPath);
 
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
         var relFile = Some.Name();
         var filePath = Path.Join(repo.LocalDirectoryPath, relFile);
 
@@ -99,7 +103,7 @@ public async Task WaitForConflictResolution_WhenMergeCompletes_ReturnsCompleted(
             RunGit(repo.LocalDirectoryPath, "commit -m resolved-merge");
         });
 
-        var result = await ConflictResolutionDetector.WaitForConflictResolution(
+        var result = await conflictResolutionDetector.WaitForConflictResolution(
             git,
             logger,
             ConflictOperationType.Merge,
@@ -144,7 +148,9 @@ public async Task WaitForConflictResolution_WhenMergeAborted_ReturnsAborted()
         // Abort after delay
         var aborter = Task.Run(async () => { await Task.Delay(60); git.AbortMerge(); });
 
-        var result = await ConflictResolutionDetector.WaitForConflictResolution(
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
+        var result = await conflictResolutionDetector.WaitForConflictResolution(
             git,
             logger,
             ConflictOperationType.Merge,
@@ -186,8 +192,10 @@ public async Task WaitForConflictResolution_WhenTimeoutReached_ReturnsTimeout()
         git.ChangeBranch(branchBase);
         try { git.MergeFromLocalSourceBranch(branchOther); } catch (ConflictException) { }
 
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
         // Do not resolve or abort; should timeout
-        var result = await ConflictResolutionDetector.WaitForConflictResolution(
+        var result = await conflictResolutionDetector.WaitForConflictResolution(
             git,
             logger,
             ConflictOperationType.Merge,
@@ -225,12 +233,14 @@ public async Task WaitForConflictResolution_WhenCancelled_Throws()
         repo.Stage(relFile);
         repo.Commit();
 
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
         // start rebase that will conflict
         try { git.RebaseFromLocalSourceBranch(branchBase); } catch (ConflictException) { }
 
         using var cts = new CancellationTokenSource();
         cts.CancelAfter(50);
-        var act = async () => await ConflictResolutionDetector.WaitForConflictResolution(
+        var act = async () => await conflictResolutionDetector.WaitForConflictResolution(
             git,
             logger,
             ConflictOperationType.Rebase,
@@ -268,6 +278,8 @@ public async Task WaitForConflictResolution_WhenRebaseCompletes_ReturnsCompleted
         repo.Stage(relFile);
         repo.Commit();
 
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
         git.ChangeBranch(featureBranch);
         try { git.RebaseFromLocalSourceBranch(baseBranch); } catch (ConflictException) { }
 
@@ -299,7 +311,7 @@ public async Task WaitForConflictResolution_WhenRebaseCompletes_ReturnsCompleted
             }
         });
 
-        var result = await ConflictResolutionDetector.WaitForConflictResolution(
+        var result = await conflictResolutionDetector.WaitForConflictResolution(
             git,
             logger,
             ConflictOperationType.Rebase,
@@ -338,12 +350,14 @@ public async Task WaitForConflictResolution_WhenRebaseAborted_ReturnsAborted()
         repo.Stage(relFile);
         repo.Commit();
 
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
         git.ChangeBranch(featureBranch);
         try { git.RebaseFromLocalSourceBranch(baseBranch); } catch (ConflictException) { }
 
         var aborter = Task.Run(async () => { await Task.Delay(60); git.AbortRebase(); });
 
-        var result = await ConflictResolutionDetector.WaitForConflictResolution(
+        var result = await conflictResolutionDetector.WaitForConflictResolution(
             git,
             logger,
             ConflictOperationType.Rebase,
diff --git a/src/Stack.Tests/Helpers/TestGitRepositoryBuilder.cs b/src/Stack.Tests/Helpers/TestGitRepositoryBuilder.cs
index 9a48e73c..025a399f 100644
--- a/src/Stack.Tests/Helpers/TestGitRepositoryBuilder.cs
+++ b/src/Stack.Tests/Helpers/TestGitRepositoryBuilder.cs
@@ -372,12 +372,28 @@ public LibGit2Sharp.Commit GetTipOfRemoteBranch(string branchName)
         return [.. LocalRepository.Branches];
     }
 
+    public LibGit2Sharp.Branch ChangeBranch(string branchName)
+    {
+        return LibGit2Sharp.Commands.Checkout(LocalRepository, branchName);
+    }
+
     public LibGit2Sharp.Commit Commit(string? message = null)
     {
         var signature = new Signature(Some.Name(), Some.Name(), DateTimeOffset.Now);
         return LocalRepository.Commit(message ?? Some.Name(), signature, signature);
     }
 
+    public LibGit2Sharp.Commit Commit(string relativePath, string contents, string? message = null)
+    {
+        var fullPath = Path.Combine(LocalDirectoryPath, relativePath);
+        Directory.CreateDirectory(Path.GetDirectoryName(fullPath)!);
+        File.WriteAllText(fullPath, contents);
+        LibGit2Sharp.Commands.Stage(LocalRepository, relativePath);
+
+        var signature = new Signature(Some.Name(), Some.Name(), DateTimeOffset.Now);
+        return LocalRepository.Commit(message ?? Some.Name(), signature, signature);
+    }
+
     public void Stage(string path)
     {
         LibGit2Sharp.Commands.Stage(LocalRepository, path);
@@ -445,6 +461,54 @@ public void CreateCommitOnRemoteTrackingBranch(string branchName, string message
         LocalRepository.Refs.UpdateTarget(remoteBranch.Reference, commit.Id);
     }
 
+    /// <summary>
+    /// Creates a "squash merge" style commit on the target branch whose tree matches the tip of the branch being squashed.
+    /// This simulates a PR being squash merged into the target branch (e.g. source) without preserving the original commits.
+    /// The newly created commit is added to both the local and remote tracking refs of the target branch (if a remote exists).
+    /// </summary>
+    /// <param name="branchToSquashName">The feature/stack branch whose cumulative changes will be squashed.</param>
+    /// <param name="targetBranchName">The branch to receive the squash commit (typically the source branch).</param>
+    /// <param name="message">The commit message for the squash commit.</param>
+    /// <returns>The created squash commit.</returns>
+    public LibGit2Sharp.Commit CreateSquashCommitFromBranchOntoBranch(string branchToSquashName, string targetBranchName, string message)
+    {
+        var branchToSquash = LocalRepository.Branches[branchToSquashName];
+        var targetBranch = LocalRepository.Branches[targetBranchName];
+
+        if (branchToSquash is null)
+        {
+            throw new ArgumentException($"Branch '{branchToSquashName}' does not exist", nameof(branchToSquashName));
+        }
+
+        if (targetBranch is null)
+        {
+            throw new ArgumentException($"Target branch '{targetBranchName}' does not exist", nameof(targetBranchName));
+        }
+
+        var signature = new Signature(Some.Name(), Some.Email(), DateTimeOffset.Now);
+        var parent = targetBranch.Tip;
+        var tree = branchToSquash.Tip.Tree; // Use the full tree of the branch being squashed
+
+        var squashCommit = LocalRepository.ObjectDatabase.CreateCommit(
+            signature,
+            signature,
+            message,
+            tree,
+            new[] { parent },
+            false);
+
+        // Fast-forward the local target branch to the squash commit
+        LocalRepository.Refs.UpdateTarget(targetBranch.Reference, squashCommit.Id);
+
+        // Fast-forward the remote tracking branch if it exists
+        if (targetBranch.TrackedBranch is not null)
+        {
+            LocalRepository.Refs.UpdateTarget(targetBranch.TrackedBranch.Reference, squashCommit.Id);
+        }
+
+        return squashCommit;
+    }
+
     public Worktree CreateWorktree(string branchName)
     {
         // Validate branch exists
diff --git a/src/Stack.Tests/Integration/StackActionsTests.cs b/src/Stack.Tests/Integration/StackActionsTests.cs
index 5ac7e682..735802df 100644
--- a/src/Stack.Tests/Integration/StackActionsTests.cs
+++ b/src/Stack.Tests/Integration/StackActionsTests.cs
@@ -24,26 +24,25 @@ public void PullChanges_WhenChangesExistOnSourceAndBranchInStack_PullsChangesCor
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Create commits on remote tracking branches to simulate changes to pull
         repo.CreateCommitOnRemoteTrackingBranch(sourceBranch, "Remote change on source");
         repo.CreateCommitOnRemoteTrackingBranch(otherBranch, "Remote change on other");
 
         // Make source branch current
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
 
         var stack = new TestStackBuilder()
             .WithSourceBranch(sourceBranch)
             .WithBranch(b => b.WithName(otherBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -71,18 +70,17 @@ public void PullChanges_WhenChangesExistOnWorktreeBranch_PullsChangesCorrectly()
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Create commits on remote tracking branch to simulate changes to pull  
         repo.CreateCommitOnRemoteTrackingBranch(worktreeBranch, "Remote change on worktree branch");
 
         // Switch to source branch first, then create worktree (can't create worktree for current branch)
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
 
         // Create a worktree for the branch
         var worktreePath = repo.CreateWorktree(worktreeBranch);
@@ -92,7 +90,7 @@ public void PullChanges_WhenChangesExistOnWorktreeBranch_PullsChangesCorrectly()
             .WithBranch(b => b.WithName(worktreeBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -116,14 +114,13 @@ public void PullChanges_WhenLocalBranchHasNoRemoteTrackingBranch_DoesNotPullChan
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
         var initialLocalTip = repo.GetTipOfBranch(localOnlyBranch);
 
         var stack = new TestStackBuilder()
@@ -131,7 +128,7 @@ public void PullChanges_WhenLocalBranchHasNoRemoteTrackingBranch_DoesNotPullChan
             .WithBranch(b => b.WithName(localOnlyBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -154,17 +151,16 @@ public void PullChanges_WhenRemoteTrackingBranchIsDeleted_DoesNotPullChanges()
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Delete the remote tracking branch to simulate deleted remote
         repo.DeleteRemoteTrackingBranch(deletedRemoteBranch);
 
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
         var initialLocalTip = repo.GetTipOfBranch(deletedRemoteBranch);
 
         var stack = new TestStackBuilder()
@@ -172,7 +168,7 @@ public void PullChanges_WhenRemoteTrackingBranchIsDeleted_DoesNotPullChanges()
             .WithBranch(b => b.WithName(deletedRemoteBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PullChanges(stack);
@@ -199,22 +195,21 @@ public async Task UpdateStack_WhenUpdatingUsingMerge_AndChangesExistOnMultipleBr
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Add changes to source branch (simulating changes to merge)
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
         var filePath = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath, "source change");
         repo.Stage(Path.GetFileName(filePath));
         var sourceCommit = repo.Commit("Source branch change");
 
         // Add changes to line1Branch1 (simulating changes at multiple levels)
-        gitClient.ChangeBranch(line1Branch1);
+        repo.ChangeBranch(line1Branch1);
         var filePath2 = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath2, "line1 change");
         repo.Stage(Path.GetFileName(filePath2));
@@ -226,7 +221,7 @@ public async Task UpdateStack_WhenUpdatingUsingMerge_AndChangesExistOnMultipleBr
             .WithBranch(b => b.WithName(line2Branch1))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         await stackActions.UpdateStack(stack, UpdateStrategy.Merge, CancellationToken.None);
@@ -257,22 +252,21 @@ public async Task UpdateStack_WhenUpdatingUsingRebase_AndChangesExistOnMultipleB
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Add changes to source branch (simulating changes to rebase onto)
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
         var filePath = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath, "source change");
         repo.Stage(Path.GetFileName(filePath));
         var sourceCommit = repo.Commit("Source branch change");
 
         // Add changes to line1Branch1 (simulating changes at multiple levels)
-        gitClient.ChangeBranch(line1Branch1);
+        repo.ChangeBranch(line1Branch1);
         var filePath2 = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath2, "line1 change");
         repo.Stage(Path.GetFileName(filePath2));
@@ -284,7 +278,7 @@ public async Task UpdateStack_WhenUpdatingUsingRebase_AndChangesExistOnMultipleB
             .WithBranch(b => b.WithName(line2Branch1))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
@@ -317,22 +311,21 @@ public async Task UpdateStack_WhenUpdatingUsingMerge_AndBranchCheckedOutInWorktr
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Add change to source
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
         var sourceFile = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(sourceFile, "source change");
         repo.Stage(Path.GetFileName(sourceFile));
         var sourceCommit = repo.Commit("Source branch change");
 
         // Add change to parent branch
-        gitClient.ChangeBranch(parentBranch);
+        repo.ChangeBranch(parentBranch);
         var parentFile = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(parentFile, "parent change");
         repo.Stage(Path.GetFileName(parentFile));
@@ -343,11 +336,11 @@ public async Task UpdateStack_WhenUpdatingUsingMerge_AndBranchCheckedOutInWorktr
             .WithBranch(b => b.WithName(parentBranch).WithChildBranch(c => c.WithName(childBranch)))
             .Build();
 
-        gitClient.ChangeBranch(sourceBranch); // ensure not on child
+        repo.ChangeBranch(sourceBranch); // ensure not on child
         var worktree = repo.CreateWorktree(childBranch);
         worktree.Should().NotBeNull();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         await stackActions.UpdateStack(stack, UpdateStrategy.Merge, CancellationToken.None);
@@ -373,22 +366,21 @@ public async Task UpdateStack_WhenUpdatingUsingRebase_AndBranchCheckedOutInWorkt
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Add change to source
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
         var sourceFile = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(sourceFile, "source change");
         repo.Stage(Path.GetFileName(sourceFile));
         var sourceCommit = repo.Commit("Source branch change");
 
         // Add change to parent
-        gitClient.ChangeBranch(parentBranch);
+        repo.ChangeBranch(parentBranch);
         var parentFile = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(parentFile, "parent change");
         repo.Stage(Path.GetFileName(parentFile));
@@ -399,11 +391,11 @@ public async Task UpdateStack_WhenUpdatingUsingRebase_AndBranchCheckedOutInWorkt
             .WithBranch(b => b.WithName(parentBranch).WithChildBranch(c => c.WithName(childBranch)))
             .Build();
 
-        gitClient.ChangeBranch(sourceBranch); // ensure not on child
+        repo.ChangeBranch(sourceBranch); // ensure not on child
         var worktreePath = repo.CreateWorktree(childBranch);
         worktreePath.Should().NotBeNull();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
@@ -414,6 +406,144 @@ public async Task UpdateStack_WhenUpdatingUsingRebase_AndBranchCheckedOutInWorkt
         childCommits.Should().Contain(c => c.MessageShort == "Parent branch change", "child branch should contain parent changes after rebase (message match due to rewritten SHA)");
     }
 
+    [Fact]
+    public async Task UpdateStack_WhenUpdatingUsingRebase_AndFirstBranchWasSquashMerged_ReparentsOntoSourceBranchToAvoidConflicts()
+    {
+        // Arrange
+        var sourceBranch = Some.BranchName();
+        var firstBranch = Some.BranchName();
+        var secondBranch = Some.BranchName();
+        var thirdBranch = Some.BranchName();
+        var fourthBranch = Some.BranchName();
+
+        using var repo = new TestGitRepositoryBuilder()
+            .WithBranch(builder => builder.WithName(sourceBranch).PushToRemote().WithNumberOfEmptyCommits(1))
+            .WithBranch(builder => builder.WithName(firstBranch).FromSourceBranch(sourceBranch).WithNumberOfEmptyCommits(3).PushToRemote())
+            .WithBranch(builder => builder.WithName(secondBranch).FromSourceBranch(firstBranch).WithNumberOfEmptyCommits(1).PushToRemote())
+            .WithBranch(builder => builder.WithName(thirdBranch).FromSourceBranch(secondBranch).WithNumberOfEmptyCommits(1).PushToRemote())
+            .WithBranch(builder => builder.WithName(fourthBranch).FromSourceBranch(secondBranch).WithNumberOfEmptyCommits(1).PushToRemote())
+            .Build();
+
+        var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var gitHubClient = Substitute.For<IGitHubClient>();
+        var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
+        var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
+        var tipOfFirstBranch = repo.GetTipOfBranch(firstBranch);
+
+        // Simulate squash merge of the first branch into the source branch on the remote (keeping first branch locally untouched)
+        repo.ChangeBranch(sourceBranch);
+        var squashCommit = repo.CreateSquashCommitFromBranchOntoBranch(firstBranch, sourceBranch, "Squash merge first branch");
+
+        // Delete the remote tracking branch for firstBranch to simulate PR being closed/merged & branch deleted
+        repo.DeleteRemoteTrackingBranch(firstBranch);
+
+        var stack = new TestStackBuilder()
+            .WithSourceBranch(sourceBranch)
+            .WithBranch(b => b.WithName(firstBranch)
+                .WithChildBranch(c => c.WithName(secondBranch)
+                    .WithChildBranch(d => d.WithName(thirdBranch))
+                    .WithChildBranch(e => e.WithName(fourthBranch))))
+            .Build();
+
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
+
+        // Act
+        await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
+
+        // Assert
+        var secondBranchCommits = repo.GetCommitsReachableFromBranch(secondBranch);
+        var thirdBranchCommits = repo.GetCommitsReachableFromBranch(thirdBranch);
+        var fourthBranchCommits = repo.GetCommitsReachableFromBranch(fourthBranch);
+
+        secondBranchCommits.Should().Contain(c => c.Sha == squashCommit.Sha, "Second branch should contain squash commit from source");
+        thirdBranchCommits.Should().Contain(c => c.Sha == squashCommit.Sha, "Third branch should contain squash commit from source");
+        fourthBranchCommits.Should().Contain(c => c.Sha == squashCommit.Sha, "Fourth branch should contain squash commit from source");
+        secondBranchCommits.Should().NotContain(c => c.Sha == tipOfFirstBranch.Sha, "Second branch should not contain tip commit from first branch");
+        thirdBranchCommits.Should().NotContain(c => c.Sha == tipOfFirstBranch.Sha, "Third branch should not contain tip commit from first branch");
+        fourthBranchCommits.Should().NotContain(c => c.Sha == tipOfFirstBranch.Sha, "Fourth branch should not contain tip commit from first branch");
+
+        repo.CreateCommitOnRemoteTrackingBranch(sourceBranch, "New commit on source after squash merge");
+        var tipOfSourceAfterNewCommit = repo.GetTipOfBranch(sourceBranch);
+
+        // Act again to verify subsequent rebase still works
+        await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
+
+        secondBranchCommits = repo.GetCommitsReachableFromBranch(secondBranch);
+        thirdBranchCommits = repo.GetCommitsReachableFromBranch(thirdBranch);
+        fourthBranchCommits = repo.GetCommitsReachableFromBranch(fourthBranch);
+        secondBranchCommits.Should().Contain(c => c.Sha == tipOfSourceAfterNewCommit.Sha, "Second branch should contain latest commit from source after subsequent rebase");
+        thirdBranchCommits.Should().Contain(c => c.Sha == tipOfSourceAfterNewCommit.Sha, "Third branch should contain latest commit from source after subsequent rebase");
+        fourthBranchCommits.Should().Contain(c => c.Sha == tipOfSourceAfterNewCommit.Sha, "Fourth branch should contain latest commit from source after subsequent rebase");
+    }
+
+    [Fact]
+    public async Task UpdateStack_WhenUpdatingUsingRebase_AndFirstBranchWasSquashMergedWithAdditionalCommitsNotMergedIntoChildren_ReparentsOntoSourceBranchToAvoidConflicts()
+    {
+        // Arrange
+        var sourceBranch = Some.BranchName();
+        var firstBranch = Some.BranchName();
+        var secondBranch = Some.BranchName();
+        var thirdBranch = Some.BranchName();
+        var fourthBranch = Some.BranchName();
+
+        using var repo = new TestGitRepositoryBuilder()
+            .WithBranch(builder => builder.WithName(sourceBranch).PushToRemote().WithNumberOfEmptyCommits(1))
+            .WithBranch(builder => builder.WithName(firstBranch).FromSourceBranch(sourceBranch).WithNumberOfEmptyCommits(3).PushToRemote())
+            .WithBranch(builder => builder.WithName(secondBranch).FromSourceBranch(firstBranch).WithNumberOfEmptyCommits(1).PushToRemote())
+            .WithBranch(builder => builder.WithName(thirdBranch).FromSourceBranch(secondBranch).WithNumberOfEmptyCommits(1).PushToRemote())
+            .WithBranch(builder => builder.WithName(fourthBranch).FromSourceBranch(secondBranch).WithNumberOfEmptyCommits(1).PushToRemote())
+            .Build();
+
+        var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
+        var displayProvider = new TestDisplayProvider(testOutputHelper);
+        var gitHubClient = Substitute.For<IGitHubClient>();
+        var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
+        var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
+
+        // Add another commit to the first branch that isn't in the children
+        repo.ChangeBranch(firstBranch);
+        repo.Commit("file.txt", Some.Name(), "Additional commit on first branch not in children");
+        repo.Push(firstBranch);
+
+        var tipOfFirstBranch = repo.GetTipOfBranch(firstBranch);
+
+        // Simulate squash merge of the first branch into the source branch on the remote (keeping first branch locally untouched)
+        repo.ChangeBranch(sourceBranch);
+        var squashCommit = repo.CreateSquashCommitFromBranchOntoBranch(firstBranch, sourceBranch, "Squash merge first branch");
+
+        // Delete the remote tracking branch for firstBranch to simulate PR being closed/merged & branch deleted
+        repo.DeleteRemoteTrackingBranch(firstBranch);
+
+        var stack = new TestStackBuilder()
+            .WithSourceBranch(sourceBranch)
+            .WithBranch(b => b.WithName(firstBranch)
+                .WithChildBranch(c => c.WithName(secondBranch)
+                    .WithChildBranch(d => d.WithName(thirdBranch))
+                    .WithChildBranch(e => e.WithName(fourthBranch))))
+            .Build();
+
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
+
+        // Act
+        await stackActions.UpdateStack(stack, UpdateStrategy.Rebase, CancellationToken.None);
+
+        // Assert
+        var secondBranchCommits = repo.GetCommitsReachableFromBranch(secondBranch);
+        var thirdBranchCommits = repo.GetCommitsReachableFromBranch(thirdBranch);
+        var fourthBranchCommits = repo.GetCommitsReachableFromBranch(fourthBranch);
+
+        secondBranchCommits.Should().Contain(c => c.Sha == squashCommit.Sha, "Second branch should contain squash commit from source");
+        thirdBranchCommits.Should().Contain(c => c.Sha == squashCommit.Sha, "Third branch should contain squash commit from source");
+        fourthBranchCommits.Should().Contain(c => c.Sha == squashCommit.Sha, "Fourth branch should contain squash commit from source");
+        secondBranchCommits.Should().NotContain(c => c.Sha == tipOfFirstBranch.Sha, "Second branch should not contain tip commit from first branch");
+        thirdBranchCommits.Should().NotContain(c => c.Sha == tipOfFirstBranch.Sha, "Third branch should not contain tip commit from first branch");
+        fourthBranchCommits.Should().NotContain(c => c.Sha == tipOfFirstBranch.Sha, "Fourth branch should not contain tip commit from first branch");
+    }
+
     [Fact]
     public void PushChanges_WhenChangesExistOnCurrentBranch_PushesChangesCorrectly()
     {
@@ -427,15 +557,14 @@ public void PushChanges_WhenChangesExistOnCurrentBranch_PushesChangesCorrectly()
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Make changes to the current branch
-        gitClient.ChangeBranch(currentBranch);
+        repo.ChangeBranch(currentBranch);
         var filePath = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath, "local change");
         repo.Stage(Path.GetFileName(filePath));
@@ -448,7 +577,7 @@ public void PushChanges_WhenChangesExistOnCurrentBranch_PushesChangesCorrectly()
             .WithBranch(b => b.WithName(currentBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, 5, false);
@@ -472,22 +601,21 @@ public void PushChanges_WhenChangesExistOnNonCurrentBranch_PushesChangesCorrectl
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Make changes to the non-current branch
-        gitClient.ChangeBranch(nonCurrentBranch);
+        repo.ChangeBranch(nonCurrentBranch);
         var filePath = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath, "local change");
         repo.Stage(Path.GetFileName(filePath));
         var localCommit = repo.Commit("Local change on non-current branch");
 
         // Switch to source branch so nonCurrentBranch is non-current
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
         var initialRemoteCommitCount = repo.GetCommitsReachableFromRemoteBranch(nonCurrentBranch).Count;
 
         var stack = new TestStackBuilder()
@@ -495,7 +623,7 @@ public void PushChanges_WhenChangesExistOnNonCurrentBranch_PushesChangesCorrectl
             .WithBranch(b => b.WithName(nonCurrentBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, 5, false);
@@ -519,22 +647,21 @@ public void PushChanges_WhenChangesExistOnWorktreeBranch_PushesChangesCorrectly(
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Make changes to the worktree branch, then switch away to create worktree
-        gitClient.ChangeBranch(worktreeBranch);
+        repo.ChangeBranch(worktreeBranch);
         var filePath = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath, "worktree branch change");
         repo.Stage(Path.GetFileName(filePath));
         var branchCommit = repo.Commit("Change in worktree branch");
 
         // Switch to source branch first, then create worktree (can't create worktree for current branch)
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
 
         // Create a worktree for the branch
         var worktreePath = repo.CreateWorktree(worktreeBranch);
@@ -544,7 +671,7 @@ public void PushChanges_WhenChangesExistOnWorktreeBranch_PushesChangesCorrectly(
             .WithBranch(b => b.WithName(worktreeBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act
         stackActions.PushChanges(stack, 5, false);
@@ -568,21 +695,20 @@ public void PushChanges_WhenLocalOnlyBranchExists_CreatesRemoteTrackingBranch()
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Make changes to the local-only branch
-        gitClient.ChangeBranch(localOnlyBranch);
+        repo.ChangeBranch(localOnlyBranch);
         var filePath = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath, "local change");
         repo.Stage(Path.GetFileName(filePath));
         var localCommit = repo.Commit("Local change on local-only branch");
 
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
 
         // Verify initially no remote tracking branch
         var initialHasRemoteTracking = repo.DoesRemoteBranchExist(localOnlyBranch);
@@ -593,16 +719,15 @@ public void PushChanges_WhenLocalOnlyBranchExists_CreatesRemoteTrackingBranch()
             .WithBranch(b => b.WithName(localOnlyBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act - should complete without errors and should actually create the remote tracking branch
         stackActions.PushChanges(stack, 5, false);
 
         // Assert - verify branch exists locally and now HAS a remote tracking branch (because PushChanges creates it)
-        var branchExists = gitClient.DoesLocalBranchExist(localOnlyBranch);
+        var tipOfBranch = repo.GetTipOfBranch(localOnlyBranch); // Throws if branch doesn't exist
         var finalHasRemoteTracking = repo.DoesRemoteBranchExist(localOnlyBranch);
 
-        branchExists.Should().BeTrue("local branch should still exist");
         finalHasRemoteTracking.Should().BeTrue("PushChanges should create remote tracking branch for branches without one");
 
         // Also assert that the remote branch has the correct SHA from the local branch
@@ -624,15 +749,14 @@ public void PushChanges_WhenRemoteTrackingBranchHasBeenDeleted_DoesNotPushChange
             .Build();
 
         var logger = XUnitLogger.CreateLogger<StackActions>(testOutputHelper);
-        var gitClientLogger = XUnitLogger.CreateLogger<GitClient>(testOutputHelper);
         var displayProvider = new TestDisplayProvider(testOutputHelper);
-        var gitClient = new GitClient(gitClientLogger, repo.LocalDirectoryPath);
         var gitHubClient = Substitute.For<IGitHubClient>();
         var cliExecutionContext = new CliExecutionContext() { WorkingDirectory = repo.LocalDirectoryPath };
         var gitClientFactory = new TestGitClientFactory(testOutputHelper);
+        var conflictResolutionDetector = new ConflictResolutionDetector();
 
         // Make changes to the branch
-        gitClient.ChangeBranch(deletedRemoteBranch);
+        repo.ChangeBranch(deletedRemoteBranch);
         var filePath = Path.Join(repo.LocalDirectoryPath, Some.Name());
         File.WriteAllText(filePath, "local change");
         repo.Stage(Path.GetFileName(filePath));
@@ -641,7 +765,7 @@ public void PushChanges_WhenRemoteTrackingBranchHasBeenDeleted_DoesNotPushChange
         // Delete the remote tracking branch to simulate deleted remote
         repo.DeleteRemoteTrackingBranch(deletedRemoteBranch);
 
-        gitClient.ChangeBranch(sourceBranch);
+        repo.ChangeBranch(sourceBranch);
         var initialLocalCommitCount = repo.GetCommitsReachableFromBranch(deletedRemoteBranch).Count;
 
         var stack = new TestStackBuilder()
@@ -649,7 +773,7 @@ public void PushChanges_WhenRemoteTrackingBranchHasBeenDeleted_DoesNotPushChange
             .WithBranch(b => b.WithName(deletedRemoteBranch))
             .Build();
 
-        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider);
+        var stackActions = new StackActions(gitClientFactory, cliExecutionContext, gitHubClient, logger, displayProvider, conflictResolutionDetector);
 
         // Act - should complete without errors even with deleted remote
         stackActions.PushChanges(stack, 5, false);
diff --git a/src/Stack/Commands/Helpers/StackActions.cs b/src/Stack/Commands/Helpers/StackActions.cs
index eceb1b8c..b3a9994f 100644
--- a/src/Stack/Commands/Helpers/StackActions.cs
+++ b/src/Stack/Commands/Helpers/StackActions.cs
@@ -20,7 +20,8 @@ public class StackActions(
         CliExecutionContext executionContext,
         IGitHubClient gitHubClient,
         ILogger<StackActions> logger,
-        IDisplayProvider displayProvider) : IStackActions
+        IDisplayProvider displayProvider,
+        IConflictResolutionDetector conflictResolutionDetector) : IStackActions
     {
         /// <summary>
         /// Gets the default GitClient for the current working directory
@@ -216,7 +217,7 @@ private async Task MergeFromSourceBranch(string branch, string sourceBranchName,
             }
             catch (ConflictException)
             {
-                var result = await ConflictResolutionDetector.WaitForConflictResolution(
+                var result = await conflictResolutionDetector.WaitForConflictResolution(
                     branchGitClient,
                     logger,
                     ConflictOperationType.Merge,
@@ -233,8 +234,7 @@ private async Task MergeFromSourceBranch(string branch, string sourceBranchName,
                     case ConflictResolutionResult.Timeout:
                         throw new TimeoutException("Timed out waiting for merge conflict resolution.");
                     case ConflictResolutionResult.NotStarted:
-                        logger.LogWarning("Expected merge to be in progress but marker not found. Proceeding cautiously.");
-                        break;
+                        throw new Exception("Expected merge to be in progress but it is not. Use --verbose output for more details.");
                 }
             }
         }
@@ -258,89 +258,146 @@ private async Task UpdateStackUsingRebase(
         private async Task UpdateBranchLineUsingRebase(StackStatus status, List<BranchDetail> branchLine, Dictionary<string, GitBranchStatus> branchStatuses, CancellationToken cancellationToken)
         {
             //
-            // When rebasing the stack, we'll use `git rebase --update-refs` from the
-            // lowest branch in the stack to pick up changes throughout all branches in the stack.
-            // Because there could be changes in any branch in the stack that aren't in the ones
-            // below it, we'll repeat this all the way from the bottom to the top of the stack to
-            // ensure that all changes are applied in the correct order.
+            // When rebasing the stack, we need to be able to pick up changes at each level of the stack.
+            // 
+            // We need to handle a few specific scenarios:
+            // - When one of the branches has been squash merged into the source branch.
+            // - When a branch has additional commits that weren't rebased into children before merging into the source branch.
+            //
+            // The approach we'll take it is to rebase each branch at each level of the stack against
+            // all active branches above it in the stack. 
+            //
+            // # Squash merges
+            //
+            // Squash merges are tricky:
+            // - The branch that was squash merged will have one or more commits that are going to squashed into the source branch.
+            // - Child branches will also have these commits.
+            // - When the parent branch is squash merged, the child branches will still have the set of commits that 
+            //   are equal to the contents of the squashed commit on the source branch.
+            // - When we try and rebase the child branch we hit conflicts as we try and re-apply all
+            //   the individual commits. If the commit happens to exactly match the final squashed commit it 
+            //   might work, but this is unlikely in practice, especially if the branch had multiple commits.
+            //
+            // We can detect if a branch has been squash merged into the source branch by:
+            // - Finding the common base between the branch we're rebasing and it's parent branch that was squash merged.
+            //    - Finding the common base handles the case when additional commits were made to the branch before it was squash merged.
+            // - Checking if that common base exists in the source branch. If it doesn't, then we know that it was squash merged.
+            //
+            // If we find that a branch was squash merged, we rebase directly onto the source branch, telling Git to start
+            // from the common base to ignore commits up to that point:
+            // `git rebase --onto {sourceBranch} {commonBaseBetweenChildAndOldParentBranch}`
             //
-            // For example if we have a stack like this:
-            // main -> feature1 -> feature2 -> feature3
+            // # Example
+            //
+            // With the following stack:
             // 
-            // We'll rebase feature3 onto feature2, then feature3 onto feature1, and finally feature3 onto main.
+            // main 
+            //   |-feature1 (deleted in remote - squash merged into main)
+            //     |- feature2
+            //       |- feature3
+            //       |- feature4
+            //     |- feature5
             //
-            // In addition to this, if the stack is in a state where one of the branches has been squash merged
-            // into the source branch, we'll want to rebase onto that branch directly using
-            // `git rebase --onto {sourceBranch} {oldParentBranch}` to ensure that the changes are 
-            // applied correctly and to try and avoid merge conflicts during the rebase.
+            // We'll rebase in the following order:
             // 
-            // For example if we have a stack like this:
-            // main
-            //   -> feature1 (deleted in remote): Squash merged into main
-            //   -> feature2
-            //   -> feature3
-            //  
-            // We'll rebase feature3 onto feature2 using a normal `git rebase feature2 --update-refs`, 
-            // then feature3 onto main using `git rebase --onto main feature1 --update-refs` to replay
-            // all commits from feature3 (and therefore from feature2) on top of the latest commits of main
-            // which will include the squashed commit.
+            // - feature2 onto main (re-parenting as feature1 was squash merged)
+            // - feature3 onto main (re-parenting as feature1 was squash merged)
+            // - feature3 onto feature2
+            // - feature4 onto main (re-parenting as feature1 was squash merged)
+            // - feature4 onto feature2
+            // - feature5 onto main (re-parenting as feature1 was squash merged)
             //
             logger.RebasingStackForBranchLine(status.Name, status.SourceBranch.Name, string.Join(" -> ", branchLine.Select(b => b.Name)));
+            List<BranchDetailBase> allBranchesInLine = [status.SourceBranch, .. branchLine];
 
-            BranchDetail? lowestActionBranch = null;
             foreach (var branch in branchLine)
             {
-                if (branch.IsActive)
+                if (!branch.IsActive)
                 {
-                    lowestActionBranch = branch;
+                    logger.TraceSkippingInactiveBranch(branch.Name);
+                    continue;
                 }
-            }
 
-            if (lowestActionBranch is null)
-            {
-                logger.NoActiveBranchesFound();
-                return;
-            }
-
-            string? branchToRebaseFrom = lowestActionBranch.Name;
-            string? lowestInactiveBranchToReParentFrom = null;
-
-            List<BranchDetailBase> branchesToRebaseOnto = [.. branchLine];
-            branchesToRebaseOnto.Reverse();
-            branchesToRebaseOnto.Remove(lowestActionBranch);
-            branchesToRebaseOnto.Add(status.SourceBranch);
+                string? lowestInactiveBranchToReParentFrom = null;
+                List<BranchDetailBase> branchesToRebaseOnto = [];
 
-            List<BranchDetailBase> allBranchesInStack = [status.SourceBranch, .. branchLine];
-
-            foreach (var branchToRebaseOnto in branchesToRebaseOnto)
-            {
-                if (branchToRebaseOnto.IsActive)
+                // Find all active branches above this one to 
+                // rebase onto. Also work out if there is any that
+                // are inactive that we need to re-parent from in
+                // order to handle squash merges.
+                foreach (var branchToRebaseOnto in allBranchesInLine)
                 {
-                    var lowestInactiveBranchToReParentFromDetail = lowestInactiveBranchToReParentFrom is not null ? allBranchesInStack.First(b => b.Name == lowestInactiveBranchToReParentFrom) : null;
-                    var shouldRebaseOntoParent = lowestInactiveBranchToReParentFromDetail is not null && lowestInactiveBranchToReParentFromDetail.Exists;
-
-                    if (shouldRebaseOntoParent)
+                    if (branchToRebaseOnto.Name == branch.Name)
                     {
-                        var gitClient = GetDefaultGitClient();
-                        shouldRebaseOntoParent = gitClient.IsAncestor(branchToRebaseFrom, lowestInactiveBranchToReParentFrom!);
+                        break;
                     }
 
-                    if (shouldRebaseOntoParent)
+                    if (branchToRebaseOnto.IsActive)
                     {
-                        await RebaseOntoNewParent(branchToRebaseFrom, branchToRebaseOnto.Name, lowestInactiveBranchToReParentFrom!, branchStatuses, cancellationToken);
+                        branchesToRebaseOnto.Add(branchToRebaseOnto);
                     }
-                    else
+                    else if (lowestInactiveBranchToReParentFrom is null)
                     {
-                        await RebaseFromSourceBranch(branchToRebaseFrom, branchToRebaseOnto.Name, branchStatuses, cancellationToken);
+                        lowestInactiveBranchToReParentFrom = branchToRebaseOnto.Name;
                     }
                 }
-                else if (lowestInactiveBranchToReParentFrom is null)
+
+                foreach (var branchToRebaseOnto in branchesToRebaseOnto)
                 {
-                    lowestInactiveBranchToReParentFrom = branchToRebaseOnto.Name;
+                    var lowestInactiveBranchToReParentFromDetail = lowestInactiveBranchToReParentFrom is not null ? allBranchesInLine.First(b => b.Name == lowestInactiveBranchToReParentFrom) : null;
+                    var couldRebaseOntoParent = lowestInactiveBranchToReParentFromDetail is not null && lowestInactiveBranchToReParentFromDetail.Exists;
+                    var parentCommitToRebaseFrom = couldRebaseOntoParent ? GetCommitShaToReParentFrom(branch.Name, lowestInactiveBranchToReParentFrom!, branchToRebaseOnto.Name) : null;
+
+                    if (parentCommitToRebaseFrom is not null)
+                    {
+                        await RebaseOntoNewParent(branch.Name, branchToRebaseOnto.Name, parentCommitToRebaseFrom, branchStatuses, cancellationToken);
+                    }
+                    else
+                    {
+                        await RebaseFromSourceBranch(branch.Name, branchToRebaseOnto.Name, branchStatuses, cancellationToken);
+                    }
                 }
             }
         }
 
+        private string? GetCommitShaToReParentFrom(string branchToRebase, string lowestInactiveBranchToReParentFrom, string branchToRebaseOnto)
+        {
+            var gitClient = GetDefaultGitClient();
+
+            // Get the common base between the branch we're rebasing and
+            // the branch we could potentially re-parent from.
+            var commonBase = gitClient.GetMergeBase(branchToRebase, lowestInactiveBranchToReParentFrom);
+
+            if (commonBase is null)
+            {
+                // This should never happen, but if it does, we can't re-parent
+                // so we'll just rebase from the source branch instead.
+                return null;
+            }
+
+            logger.CommonBaseBetweenBranches(branchToRebase, lowestInactiveBranchToReParentFrom, commonBase);
+
+            // Now check if the common base exists in the branch we're rebasing onto
+            // If it does, then we know that it got merged in. If it doesn't,
+            // then we know that it got squash merged in, so we should re-parent
+            // onto the new parent branch instead.
+            var commonBaseExistsInBranchBeingRebasedOnto = gitClient.IsCommitReachableFromBranch(commonBase, branchToRebaseOnto);
+
+            if (!commonBaseExistsInBranchBeingRebasedOnto)
+            {
+                logger.CommitDoesNotExistInNewParent(commonBase, branchToRebaseOnto);
+
+                // Common base doesn't exist in the branch we're rebasing onto,
+                // so we know that it got squash merged in. We can re-parent.
+                return commonBase;
+            }
+            else
+            {
+                logger.CommitExistsInNewParent(commonBase, branchToRebaseOnto);
+                return null;
+            }
+        }
+
         private async Task RebaseFromSourceBranch(string branch, string sourceBranchName, Dictionary<string, GitBranchStatus> branchStatuses, CancellationToken cancellationToken)
         {
             await displayProvider.DisplayStatusWithSuccess($"Rebasing {branch} onto {sourceBranchName}", async ct =>
@@ -354,7 +411,7 @@ await displayProvider.DisplayStatusWithSuccess($"Rebasing {branch} onto {sourceB
                 }
                 catch (ConflictException)
                 {
-                    var result = await ConflictResolutionDetector.WaitForConflictResolution(
+                    var result = await conflictResolutionDetector.WaitForConflictResolution(
                         branchGitClient,
                         logger,
                         ConflictOperationType.Rebase,
@@ -371,8 +428,7 @@ await displayProvider.DisplayStatusWithSuccess($"Rebasing {branch} onto {sourceB
                         case ConflictResolutionResult.Timeout:
                             throw new TimeoutException("Timed out waiting for rebase conflict resolution.");
                         case ConflictResolutionResult.NotStarted:
-                            logger.LogWarning("Expected rebase to be in progress but marker not found. Proceeding cautiously.");
-                            break;
+                            throw new Exception("Expected rebase to be in progress but it is not. Use --verbose output for more details.");
                     }
                 }
             }, cancellationToken);
@@ -381,7 +437,7 @@ await displayProvider.DisplayStatusWithSuccess($"Rebasing {branch} onto {sourceB
         private async Task RebaseOntoNewParent(
             string branch,
             string newParentBranchName,
-            string oldParentBranchName,
+            string oldParentCommitSha,
             Dictionary<string, GitBranchStatus> branchStatuses,
             CancellationToken cancellationToken)
         {
@@ -392,11 +448,11 @@ private async Task RebaseOntoNewParent(
 
                 try
                 {
-                    branchGitClient.RebaseOntoNewParent(newParentBranchName, oldParentBranchName);
+                    branchGitClient.RebaseOntoNewParent(newParentBranchName, oldParentCommitSha);
                 }
                 catch (ConflictException)
                 {
-                    var result = await ConflictResolutionDetector.WaitForConflictResolution(
+                    var result = await conflictResolutionDetector.WaitForConflictResolution(
                         branchGitClient,
                         logger,
                         ConflictOperationType.Rebase,
@@ -413,8 +469,7 @@ private async Task RebaseOntoNewParent(
                         case ConflictResolutionResult.Timeout:
                             throw new TimeoutException("Timed out waiting for rebase conflict resolution.");
                         case ConflictResolutionResult.NotStarted:
-                            logger.LogWarning("Expected rebase to be in progress but marker not found. Proceeding cautiously.");
-                            break;
+                            throw new Exception("Expected rebase to be in progress but it is not. Use --verbose output for more details.");
                     }
                 }
             }, cancellationToken);
@@ -462,4 +517,13 @@ internal static partial class LoggerExtensionMethods
 
     [LoggerMessage(Level = LogLevel.Debug, Message = "Rebasing {Branch} onto new parent {NewParentBranch}")]
     public static partial void RebasingBranchOntoNewParent(this ILogger logger, string branch, string newParentBranch);
+
+    [LoggerMessage(Level = LogLevel.Debug, Message = "Common base between {SourceBranch} and {TargetBranch}: {CommitSha}")]
+    public static partial void CommonBaseBetweenBranches(this ILogger logger, string sourceBranch, string targetBranch, string commitSha);
+
+    [LoggerMessage(Level = LogLevel.Debug, Message = "Commit {CommitSha} does not exist in branch {BranchToRebaseOnto}, treating previous parent as being squash merged and re-parenting.")]
+    public static partial void CommitDoesNotExistInNewParent(this ILogger logger, string commitSha, string branchToRebaseOnto);
+
+    [LoggerMessage(Level = LogLevel.Debug, Message = "Commit {CommitSha} exists in branch {BranchToRebaseOnto}, no need to re-parent")]
+    public static partial void CommitExistsInNewParent(this ILogger logger, string commitSha, string branchToRebaseOnto);
 }
diff --git a/src/Stack/Git/ConflictResolutionDetector.cs b/src/Stack/Git/ConflictResolutionDetector.cs
index a994d211..797f0d5f 100644
--- a/src/Stack/Git/ConflictResolutionDetector.cs
+++ b/src/Stack/Git/ConflictResolutionDetector.cs
@@ -5,9 +5,20 @@ namespace Stack.Git;
 public enum ConflictOperationType { Merge, Rebase }
 public enum ConflictResolutionResult { Completed, Aborted, NotStarted, Timeout }
 
-public static class ConflictResolutionDetector
+public interface IConflictResolutionDetector
 {
-    public static async Task<ConflictResolutionResult> WaitForConflictResolution(
+    Task<ConflictResolutionResult> WaitForConflictResolution(
+        IGitClient gitClient,
+        ILogger logger,
+        ConflictOperationType operationType,
+        TimeSpan pollInterval,
+        TimeSpan? timeout,
+        CancellationToken cancellationToken);
+}
+
+public class ConflictResolutionDetector : IConflictResolutionDetector
+{
+    public async Task<ConflictResolutionResult> WaitForConflictResolution(
         IGitClient gitClient,
         ILogger logger,
         ConflictOperationType operationType,
diff --git a/src/Stack/Git/GitClient.cs b/src/Stack/Git/GitClient.cs
index be607eea..8954fdb8 100644
--- a/src/Stack/Git/GitClient.cs
+++ b/src/Stack/Git/GitClient.cs
@@ -32,6 +32,8 @@ public interface IGitClient
     string GetRootOfRepository();
     string? GetConfigValue(string key);
     bool IsAncestor(string ancestor, string descendant);
+    string? GetMergeBase(string branch1, string branch2);
+    bool IsCommitReachableFromBranch(string commitSha, string branchName);
 
     bool IsMergeInProgress();
     bool IsRebaseInProgress();
@@ -118,14 +120,14 @@ public string GetRootOfRepository()
 
     public string? GetConfigValue(string key)
     {
-        var configValue = ExecuteGitCommandAndReturnOutput($"config --get {key}", false, exitCode =>
+        var configValue = ExecuteGitCommandAndReturnOutput($"config --get {key}", false, (info, result) =>
         {
-            if (exitCode == 1)
+            if (result.ExitCode == 1)
             {
-                return null;
+                return;
             }
 
-            return new Exception("Failed to get config value.");
+            throw new Exception("Failed to get config value.");
         })?.Trim();
 
         return string.IsNullOrEmpty(configValue) ? null : configValue;
@@ -135,10 +137,9 @@ public bool IsAncestor(string ancestor, string descendant)
     {
         var isAncestor = false;
 
-        ExecuteGitCommand($"merge-base --is-ancestor {ancestor} {descendant}", false, exitCode =>
+        ExecuteGitCommand($"merge-base --is-ancestor {ancestor} {descendant}", false, (info, result) =>
         {
-            isAncestor = exitCode == 0;
-            return null;
+            isAncestor = result.ExitCode == 0;
         });
 
         return isAncestor;
@@ -148,10 +149,9 @@ public bool IsMergeInProgress()
     {
         var inProgress = true;
         // "git rev-parse -q --verify MERGE_HEAD" returns 0 when a merge is in progress
-        ExecuteGitCommand("rev-parse -q --verify MERGE_HEAD", false, exitCode =>
+        ExecuteGitCommand("rev-parse -q --verify MERGE_HEAD", false, (info, result) =>
         {
-            inProgress = exitCode == 0;
-            return null; // suppress exception
+            inProgress = result.ExitCode == 0;
         });
         return inProgress;
     }
@@ -184,17 +184,12 @@ public string GetHeadSha()
     {
         // ORIG_HEAD is updated by Git before dangerous operations (merge, rebase, reset).
         // Use quiet verify; exit code 0 when ref exists, 1 otherwise.
-        string? orig = ExecuteGitCommandAndReturnOutput("rev-parse -q --verify ORIG_HEAD", false, exitCode =>
+        string? orig = ExecuteGitCommandAndReturnOutput("rev-parse -q --verify ORIG_HEAD", false, (info, result) =>
         {
-            if (exitCode == 0)
+            if (result.ExitCode > 1)
             {
-                return null; // success
+                throw new Exception("Failed to read ORIG_HEAD");
             }
-            if (exitCode == 1)
-            {
-                return null; // ref not found; treat as null without throwing
-            }
-            return new Exception("Failed to read ORIG_HEAD");
         })?.Trim();
 
         return string.IsNullOrWhiteSpace(orig) ? null : orig;
@@ -254,40 +249,43 @@ public void DeleteLocalBranch(string branchName)
 
     public void MergeFromLocalSourceBranch(string sourceBranchName)
     {
-        ExecuteGitCommand($"merge {sourceBranchName}", false, exitCode =>
+        ExecuteGitCommand($"merge {sourceBranchName}", false, (info, result) =>
         {
-            if (exitCode > 0)
+            if (result.StandardOutput.Contains("CONFLICT", StringComparison.OrdinalIgnoreCase) ||
+                result.StandardError.Contains("CONFLICT", StringComparison.OrdinalIgnoreCase))
             {
-                return new ConflictException();
+                throw new ConflictException();
             }
 
-            return null;
+            throw new ProcessException(result.StandardError, info.FileName, info.Arguments, result.ExitCode);
         });
     }
 
     public void RebaseFromLocalSourceBranch(string sourceBranchName)
     {
-        ExecuteGitCommand($"rebase {sourceBranchName} --update-refs", false, exitCode =>
+        ExecuteGitCommand($"rebase {sourceBranchName} --update-refs", false, (info, result) =>
         {
-            if (exitCode > 0)
+            if (result.StandardOutput.Contains("CONFLICT", StringComparison.OrdinalIgnoreCase) ||
+                result.StandardError.Contains("CONFLICT", StringComparison.OrdinalIgnoreCase))
             {
-                return new ConflictException();
+                throw new ConflictException();
             }
 
-            return null;
+            throw new ProcessException(result.StandardError, info.FileName, info.Arguments, result.ExitCode);
         });
     }
 
     public void RebaseOntoNewParent(string newParentBranchName, string oldParentBranchName)
     {
-        ExecuteGitCommand($"rebase --onto {newParentBranchName} {oldParentBranchName} --update-refs", false, exitCode =>
+        ExecuteGitCommand($"rebase --onto {newParentBranchName} {oldParentBranchName} --update-refs", false, (info, result) =>
         {
-            if (exitCode > 0)
+            if (result.StandardOutput.Contains("CONFLICT", StringComparison.OrdinalIgnoreCase) ||
+                result.StandardError.Contains("CONFLICT", StringComparison.OrdinalIgnoreCase))
             {
-                return new ConflictException();
+                throw new ConflictException();
             }
 
-            return null;
+            throw new ProcessException(result.StandardError, info.FileName, info.Arguments, result.ExitCode);
         });
     }
 
@@ -303,23 +301,24 @@ public void AbortRebase()
 
     public void ContinueRebase()
     {
-        ExecuteGitCommand($"rebase --continue", false, exitCode =>
+        ExecuteGitCommand($"rebase --continue", false, (info, result) =>
         {
-            if (exitCode > 0)
+            if (result.StandardOutput.Contains("CONFLICT", StringComparison.OrdinalIgnoreCase) ||
+                result.StandardError.Contains("CONFLICT", StringComparison.OrdinalIgnoreCase))
             {
-                return new ConflictException();
+                throw new ConflictException();
             }
 
-            return null;
+            throw new ProcessException(result.StandardError, info.FileName, info.Arguments, result.ExitCode);
         });
     }
 
     private string ExecuteGitCommandAndReturnOutput(
         string command,
         bool captureStandardError = false,
-        Func<int, Exception?>? exceptionHandler = null)
+        Action<ProcessExecutionInfo, ProcessExecutionResult>? exceptionHandler = null)
     {
-        return ProcessHelpers.ExecuteProcessAndReturnOutput(
+        var result = ProcessHelpers.ExecuteProcessAndReturnOutput(
             "git",
             command,
             workingDirectory,
@@ -327,15 +326,52 @@ private string ExecuteGitCommandAndReturnOutput(
             captureStandardError,
             exceptionHandler
         );
+
+        var output = result.StandardOutput;
+
+        if (captureStandardError && !string.IsNullOrWhiteSpace(result.StandardError))
+        {
+            output += $"{Environment.NewLine}{result.StandardError}";
+        }
+
+        return output;
     }
 
     private void ExecuteGitCommand(
         string command,
         bool captureStandardError = false,
-        Func<int, Exception?>? exceptionHandler = null)
+        Action<ProcessExecutionInfo, ProcessExecutionResult>? exceptionHandler = null)
     {
         ExecuteGitCommandAndReturnOutput(command, captureStandardError, exceptionHandler);
     }
+
+    public string? GetMergeBase(string branch1, string branch2)
+    {
+        var mergeBase = ExecuteGitCommandAndReturnOutput($"merge-base {branch1} {branch2}", false, (info, result) =>
+        {
+            if (result.ExitCode > 1)
+            {
+                throw new Exception("Failed to get merge base");
+            }
+        })?.Trim();
+
+        return string.IsNullOrWhiteSpace(mergeBase) ? null : mergeBase;
+    }
+
+    public bool IsCommitReachableFromBranch(string commitSha, string branchName)
+    {
+        var branchesThatContainTheCommit = ExecuteGitCommandAndReturnOutput($"branch --contains {commitSha}", false, (info, result) =>
+        {
+            if (result.ExitCode > 1)
+            {
+                throw new Exception("Failed to check if commit is reachable from branch");
+            }
+        })?.Split(Environment.NewLine, StringSplitOptions.RemoveEmptyEntries)
+            .Select(b => b.TrimStart('*', ' ').Trim())
+            .ToArray() ?? Array.Empty<string>();
+
+        return branchesThatContainTheCommit.Contains(branchName);
+    }
 }
 
 internal static partial class LoggerExtensionMethods
diff --git a/src/Stack/Git/GitHubClient.cs b/src/Stack/Git/GitHubClient.cs
index 0ae9ee8e..8c24a020 100644
--- a/src/Stack/Git/GitHubClient.cs
+++ b/src/Stack/Git/GitHubClient.cs
@@ -111,7 +111,7 @@ public void OpenPullRequest(GitHubPullRequest pullRequest)
 
     private string ExecuteGitHubCommandAndReturnOutput(string command)
     {
-        return ProcessHelpers.ExecuteProcessAndReturnOutput(
+        var result = ProcessHelpers.ExecuteProcessAndReturnOutput(
             "gh",
             command,
             context.WorkingDirectory,
@@ -119,6 +119,8 @@ private string ExecuteGitHubCommandAndReturnOutput(string command)
             false,
             null
         );
+
+        return result.StandardOutput.Trim();
     }
 
     private void ExecuteGitHubCommand(string command)
diff --git a/src/Stack/Git/ProcessHelpers.cs b/src/Stack/Git/ProcessHelpers.cs
index 1e409d3b..4e74388f 100644
--- a/src/Stack/Git/ProcessHelpers.cs
+++ b/src/Stack/Git/ProcessHelpers.cs
@@ -6,15 +6,18 @@
 
 namespace Stack.Git;
 
+public record ProcessExecutionResult(int ExitCode, string StandardOutput, string StandardError);
+public record ProcessExecutionInfo(string FileName, string Arguments, string? WorkingDirectory);
+
 public static class ProcessHelpers
 {
-    public static string ExecuteProcessAndReturnOutput(
+    public static ProcessExecutionResult ExecuteProcessAndReturnOutput(
         string fileName,
         string command,
         string? workingDirectory,
         ILogger logger,
         bool captureStandardError = false,
-        Func<int, Exception?>? exceptionHandler = null)
+        Action<ProcessExecutionInfo, ProcessExecutionResult>? exceptionHandler = null)
     {
         logger.ExecutingCommand(fileName, command);
 
@@ -33,7 +36,7 @@ public static string ExecuteProcessAndReturnOutput(
         };
 
         using var process = Process.Start(psi);
-        if (process is null) return string.Empty;
+        if (process is null) return new ProcessExecutionResult(-1, string.Empty, string.Empty);
 
         process.OutputDataReceived += (_, e) =>
         {
@@ -49,23 +52,23 @@ public static string ExecuteProcessAndReturnOutput(
         process.BeginOutputReadLine();
 
         process.WaitForExit();
-        int result = process.ExitCode;
+        int exitCode = process.ExitCode;
+        var standardOutput = infoBuilder.ToString();
+        var standardError = errorBuilder.ToString();
+        var result = new ProcessExecutionResult(exitCode, standardOutput, standardError);
+        var info = new ProcessExecutionInfo(fileName, command, workingDirectory);
 
-        if (result != 0)
+        if (exitCode != 0)
         {
-            logger.CommandFailed(fileName, command, result, errorBuilder.ToString());
+            logger.CommandFailed(fileName, command, exitCode, errorBuilder.ToString());
 
             if (exceptionHandler != null)
             {
-                var exception = exceptionHandler(result);
-                if (exception != null)
-                {
-                    throw exception;
-                }
+                exceptionHandler(info, result);
             }
             else
             {
-                throw new ProcessException(errorBuilder.ToString(), fileName, command, result);
+                throw new ProcessException(errorBuilder.ToString(), fileName, command, exitCode);
             }
         }
 
@@ -81,7 +84,7 @@ public static string ExecuteProcessAndReturnOutput(
             output += $"{Environment.NewLine}{errorBuilder}";
         }
 
-        return output;
+        return result;
     }
 }
 
diff --git a/src/Stack/Infrastructure/HostApplicationBuilderExtensions.cs b/src/Stack/Infrastructure/HostApplicationBuilderExtensions.cs
index 6f81fca0..d40e493e 100644
--- a/src/Stack/Infrastructure/HostApplicationBuilderExtensions.cs
+++ b/src/Stack/Infrastructure/HostApplicationBuilderExtensions.cs
@@ -91,6 +91,7 @@ private static void ConfigureServices(this IServiceCollection services, string[]
             var cache = provider.GetRequiredService<IMemoryCache>();
             return new CachingGitHubClient(safe, cache);
         });
+        services.AddSingleton<IConflictResolutionDetector, ConflictResolutionDetector>();
 
         services.AddSingleton<IStackActions, StackActions>();
         RegisterCommandHandlers(services);