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diff --git a/‎docs/getting-started.md‎
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diff --git a/‎dotnet/README.md‎
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diff --git a/‎dotnet/src/Client.cs‎
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diff --git a/‎dotnet/src/SdkProtocolVersion.cs‎
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diff --git a/‎dotnet/src/Session.cs‎
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@@ -1235,7 +1235,7 @@ const session = await client.createSession({
 
 ### Customize the System Message
 
-Control the AI's behavior and personality:
+Control the AI's behavior and personality by appending instructions:
 
 ```typescript
 const session = await client.createSession({
@@ -1245,6 +1245,28 @@ const session = await client.createSession({
 });
 ```
 
+For more fine-grained control, use `mode: "customize"` to override individual sections of the system prompt while preserving the rest:
+
+```typescript
+const session = await client.createSession({
+    systemMessage: {
+        mode: "customize",
+        sections: {
+            tone: { action: "replace", content: "Respond in a warm, professional tone. Be thorough in explanations." },
+            code_change_rules: { action: "remove" },
+            guidelines: { action: "append", content: "\n* Always cite data sources" },
+        },
+        content: "Focus on financial analysis and reporting.",
+    },
+});
+```
+
+Available section IDs: `identity`, `tone`, `tool_efficiency`, `environment_context`, `code_change_rules`, `guidelines`, `safety`, `tool_instructions`, `custom_instructions`, `last_instructions`.
+
+Each override supports four actions: `replace`, `remove`, `append`, and `prepend`. Unknown section IDs are handled gracefully — content is appended to additional instructions and a warning is emitted; `remove` on unknown sections is silently ignored.
+
+See the language-specific SDK READMEs for examples in [TypeScript](../nodejs/README.md), [Python](../python/README.md), [Go](../go/README.md), and [C#](../dotnet/README.md).
+
 ---
 
 ## Connecting to an External CLI Server
 
@@ -509,6 +509,34 @@ var session = await client.CreateSessionAsync(new SessionConfig
 });
 ```
 
+#### Customize Mode
+
+Use `Mode = SystemMessageMode.Customize` to selectively override individual sections of the prompt while preserving the rest:
+
+```csharp
+var session = await client.CreateSessionAsync(new SessionConfig
+{
+    Model = "gpt-5",
+    SystemMessage = new SystemMessageConfig
+    {
+        Mode = SystemMessageMode.Customize,
+        Sections = new Dictionary<string, SectionOverride>
+        {
+            [SystemPromptSections.Tone] = new() { Action = SectionOverrideAction.Replace, Content = "Respond in a warm, professional tone. Be thorough in explanations." },
+            [SystemPromptSections.CodeChangeRules] = new() { Action = SectionOverrideAction.Remove },
+            [SystemPromptSections.Guidelines] = new() { Action = SectionOverrideAction.Append, Content = "\n* Always cite data sources" },
+        },
+        Content = "Focus on financial analysis and reporting."
+    }
+});
+```
+
+Available section IDs are defined as constants on `SystemPromptSections`: `Identity`, `Tone`, `ToolEfficiency`, `EnvironmentContext`, `CodeChangeRules`, `Guidelines`, `Safety`, `ToolInstructions`, `CustomInstructions`, `LastInstructions`.
+
+Each section override supports four actions: `Replace`, `Remove`, `Append`, and `Prepend`. Unknown section IDs are handled gracefully: content is appended to additional instructions, and `Remove` overrides are silently ignored.
+
+#### Replace Mode
+
 For full control (removes all guardrails), use `Mode = SystemMessageMode.Replace`:
 
 ```csharp
 
@@ -365,6 +365,44 @@ private async Task CleanupConnectionAsync(List<Exception>? errors)
         }
     }
 
+    private static (SystemMessageConfig? wireConfig, Dictionary<string, Func<string, Task<string>>>? callbacks) ExtractTransformCallbacks(SystemMessageConfig? systemMessage)
+    {
+        if (systemMessage?.Mode != SystemMessageMode.Customize || systemMessage.Sections == null)
+        {
+            return (systemMessage, null);
+        }
+
+        var callbacks = new Dictionary<string, Func<string, Task<string>>>();
+        var wireSections = new Dictionary<string, SectionOverride>();
+
+        foreach (var (sectionId, sectionOverride) in systemMessage.Sections)
+        {
+            if (sectionOverride.Transform != null)
+            {
+                callbacks[sectionId] = sectionOverride.Transform;
+                wireSections[sectionId] = new SectionOverride { Action = SectionOverrideAction.Transform };
+            }
+            else
+            {
+                wireSections[sectionId] = sectionOverride;
+            }
+        }
+
+        if (callbacks.Count == 0)
+        {
+            return (systemMessage, null);
+        }
+
+        var wireConfig = new SystemMessageConfig
+        {
+            Mode = systemMessage.Mode,
+            Content = systemMessage.Content,
+            Sections = wireSections
+        };
+
+        return (wireConfig, callbacks);
+    }
+
     /// <summary>
     /// Creates a new Copilot session with the specified configuration.
     /// </summary>
@@ -409,6 +447,8 @@ public async Task<CopilotSession> CreateSessionAsync(SessionConfig config, Cance
             config.Hooks.OnSessionEnd != null ||
             config.Hooks.OnErrorOccurred != null);
 
+        var (wireSystemMessage, transformCallbacks) = ExtractTransformCallbacks(config.SystemMessage);
+
         var sessionId = config.SessionId ?? Guid.NewGuid().ToString();
 
         // Create and register the session before issuing the RPC so that
@@ -424,6 +464,10 @@ public async Task<CopilotSession> CreateSessionAsync(SessionConfig config, Cance
         {
             session.RegisterHooks(config.Hooks);
         }
+        if (transformCallbacks != null)
+        {
+            session.RegisterTransformCallbacks(transformCallbacks);
+        }
         if (config.OnEvent != null)
         {
             session.On(config.OnEvent);
@@ -440,7 +484,7 @@ public async Task<CopilotSession> CreateSessionAsync(SessionConfig config, Cance
                 config.ClientName,
                 config.ReasoningEffort,
                 config.Tools?.Select(ToolDefinition.FromAIFunction).ToList(),
-                config.SystemMessage,
+                wireSystemMessage,
                 config.AvailableTools,
                 config.ExcludedTools,
                 config.Provider,
@@ -519,6 +563,8 @@ public async Task<CopilotSession> ResumeSessionAsync(string sessionId, ResumeSes
             config.Hooks.OnSessionEnd != null ||
             config.Hooks.OnErrorOccurred != null);
 
+        var (wireSystemMessage, transformCallbacks) = ExtractTransformCallbacks(config.SystemMessage);
+
         // Create and register the session before issuing the RPC so that
         // events emitted by the CLI (e.g. session.start) are not dropped.
         var session = new CopilotSession(sessionId, connection.Rpc, _logger);
@@ -532,6 +578,10 @@ public async Task<CopilotSession> ResumeSessionAsync(string sessionId, ResumeSes
         {
             session.RegisterHooks(config.Hooks);
         }
+        if (transformCallbacks != null)
+        {
+            session.RegisterTransformCallbacks(transformCallbacks);
+        }
         if (config.OnEvent != null)
         {
             session.On(config.OnEvent);
@@ -548,7 +598,7 @@ public async Task<CopilotSession> ResumeSessionAsync(string sessionId, ResumeSes
                 config.Model,
                 config.ReasoningEffort,
                 config.Tools?.Select(ToolDefinition.FromAIFunction).ToList(),
-                config.SystemMessage,
+                wireSystemMessage,
                 config.AvailableTools,
                 config.ExcludedTools,
                 config.Provider,
@@ -1222,6 +1272,7 @@ private async Task<Connection> ConnectToServerAsync(Process? cliProcess, string?
         rpc.AddLocalRpcMethod("permission.request", handler.OnPermissionRequestV2);
         rpc.AddLocalRpcMethod("userInput.request", handler.OnUserInputRequest);
         rpc.AddLocalRpcMethod("hooks.invoke", handler.OnHooksInvoke);
+        rpc.AddLocalRpcMethod("systemMessage.transform", handler.OnSystemMessageTransform);
         rpc.StartListening();
 
         // Transition state to Disconnected if the JSON-RPC connection drops
@@ -1350,6 +1401,12 @@ public async Task<HooksInvokeResponse> OnHooksInvoke(string sessionId, string ho
             return new HooksInvokeResponse(output);
         }
 
+        public async Task<SystemMessageTransformRpcResponse> OnSystemMessageTransform(string sessionId, JsonElement sections)
+        {
+            var session = client.GetSession(sessionId) ?? throw new ArgumentException($"Unknown session {sessionId}");
+            return await session.HandleSystemMessageTransformAsync(sections);
+        }
+
         // Protocol v2 backward-compatibility adapters
 
         public async Task<ToolCallResponseV2> OnToolCallV2(string sessionId,
@@ -1685,6 +1742,7 @@ private static LogLevel MapLevel(TraceEventType eventType)
     [JsonSerializable(typeof(ResumeSessionResponse))]
     [JsonSerializable(typeof(SessionMetadata))]
     [JsonSerializable(typeof(SystemMessageConfig))]
+    [JsonSerializable(typeof(SystemMessageTransformRpcResponse))]
     [JsonSerializable(typeof(ToolCallResponseV2))]
     [JsonSerializable(typeof(ToolDefinition))]
     [JsonSerializable(typeof(ToolResultAIContent))]
 
@@ -16,8 +16,5 @@ internal static class SdkProtocolVersion
     /// <summary>
     /// Gets the SDK protocol version.
     /// </summary>
-    public static int GetVersion()
-    {
-        return Version;
-    }
+    public static int GetVersion() => Version;
 }
@@ -65,6 +65,8 @@ public sealed partial class CopilotSession : IAsyncDisposable
 
     private SessionHooks? _hooks;
     private readonly SemaphoreSlim _hooksLock = new(1, 1);
+    private Dictionary<string, Func<string, Task<string>>>? _transformCallbacks;
+    private readonly SemaphoreSlim _transformCallbacksLock = new(1, 1);
     private SessionRpc? _sessionRpc;
     private int _isDisposed;
 
@@ -653,6 +655,72 @@ internal void RegisterHooks(SessionHooks hooks)
         };
     }
 
+    /// <summary>
+    /// Registers transform callbacks for system message sections.
+    /// </summary>
+    /// <param name="callbacks">The transform callbacks keyed by section identifier.</param>
+    internal void RegisterTransformCallbacks(Dictionary<string, Func<string, Task<string>>>? callbacks)
+    {
+        _transformCallbacksLock.Wait();
+        try
+        {
+            _transformCallbacks = callbacks;
+        }
+        finally
+        {
+            _transformCallbacksLock.Release();
+        }
+    }
+
+    /// <summary>
+    /// Handles a systemMessage.transform RPC call from the Copilot CLI.
+    /// </summary>
+    /// <param name="sections">The raw JSON element containing sections to transform.</param>
+    /// <returns>A task that resolves with the transformed sections.</returns>
+    internal async Task<SystemMessageTransformRpcResponse> HandleSystemMessageTransformAsync(JsonElement sections)
+    {
+        Dictionary<string, Func<string, Task<string>>>? callbacks;
+        await _transformCallbacksLock.WaitAsync();
+        try
+        {
+            callbacks = _transformCallbacks;
+        }
+        finally
+        {
+            _transformCallbacksLock.Release();
+        }
+
+        var parsed = JsonSerializer.Deserialize(
+            sections.GetRawText(),
+            SessionJsonContext.Default.DictionaryStringSystemMessageTransformSection) ?? new();
+
+        var result = new Dictionary<string, SystemMessageTransformSection>();
+        foreach (var (sectionId, data) in parsed)
+        {
+            Func<string, Task<string>>? callback = null;
+            callbacks?.TryGetValue(sectionId, out callback);
+
+            if (callback != null)
+            {
+                try
+                {
+                    var transformed = await callback(data.Content ?? "");
+                    result[sectionId] = new SystemMessageTransformSection { Content = transformed };
+                }
+                catch
+                {
+                    result[sectionId] = new SystemMessageTransformSection { Content = data.Content ?? "" };
+                }
+            }
+            else
+            {
+                result[sectionId] = new SystemMessageTransformSection { Content = data.Content ?? "" };
+            }
+        }
+
+        return new SystemMessageTransformRpcResponse { Sections = result };
+    }
+
     /// <summary>
     /// Gets the complete list of messages and events in the session.
     /// </summary>
@@ -891,5 +959,8 @@ internal record SessionDestroyRequest
     [JsonSerializable(typeof(SessionEndHookOutput))]
     [JsonSerializable(typeof(ErrorOccurredHookInput))]
     [JsonSerializable(typeof(ErrorOccurredHookOutput))]
+    [JsonSerializable(typeof(SystemMessageTransformSection))]
+    [JsonSerializable(typeof(SystemMessageTransformRpcResponse))]
+    [JsonSerializable(typeof(Dictionary<string, SystemMessageTransformSection>))]
     internal partial class SessionJsonContext : JsonSerializerContext;
 }