diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index bca2129a..cca30e6d 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -9,6 +9,7 @@
 - Bash tool now displays the timeout value in the UI when a timeout is set ([#780](https://github.com/badlogic/pi-mono/pull/780) by [@dannote](https://github.com/dannote))
 - Export `getShellConfig` for extensions to detect user's shell environment ([#766](https://github.com/badlogic/pi-mono/pull/766) by [@dannote](https://github.com/dannote))
 - Added `thinkingText` and `selectedBg` to theme schema ([#763](https://github.com/badlogic/pi-mono/pull/763) by [@scutifer](https://github.com/scutifer))
+- `navigateTree()` now supports `replaceInstructions` option to replace the default summarization prompt entirely, and `label` option to attach a label to the branch summary entry ([#787](https://github.com/badlogic/pi-mono/pull/787) by [@mitsuhiko](https://github.com/mitsuhiko))
 
 ### Fixed
 
diff --git a/packages/coding-agent/docs/extensions.md b/packages/coding-agent/docs/extensions.md
index 5c80694b..7ef92582 100644
--- a/packages/coding-agent/docs/extensions.md
+++ b/packages/coding-agent/docs/extensions.md
@@ -733,9 +733,18 @@ Navigate to a different point in the session tree:
 ```typescript
 const result = await ctx.navigateTree("entry-id-456", {
   summarize: true,
+  customInstructions: "Focus on error handling changes",
+  replaceInstructions: false, // true = replace default prompt entirely
+  label: "review-checkpoint",
 });
 ```
 
+Options:
+- `summarize`: Whether to generate a summary of the abandoned branch
+- `customInstructions`: Custom instructions for the summarizer
+- `replaceInstructions`: If true, `customInstructions` replaces the default prompt instead of being appended
+- `label`: Label to attach to the branch summary entry (or target entry if not summarizing)
+
 ## ExtensionAPI Methods
 
 ### pi.on(event, handler)
diff --git a/packages/coding-agent/docs/sdk.md b/packages/coding-agent/docs/sdk.md
index d231b291..a2052783 100644
--- a/packages/coding-agent/docs/sdk.md
+++ b/packages/coding-agent/docs/sdk.md
@@ -110,7 +110,7 @@ interface AgentSession {
   
   // Forking
   fork(entryId: string): Promise<{ selectedText: string; cancelled: boolean }>;  // Creates new session file
-  navigateTree(targetId: string, options?: { summarize?: boolean }): Promise<{ editorText?: string; cancelled: boolean }>;  // In-place navigation
+  navigateTree(targetId: string, options?: { summarize?: boolean; customInstructions?: string; replaceInstructions?: boolean; label?: string }): Promise<{ editorText?: string; cancelled: boolean }>;  // In-place navigation
   
   // Hook message injection
   sendHookMessage(message: HookMessage, triggerTurn?: boolean): Promise<void>;
diff --git a/packages/coding-agent/docs/tree.md b/packages/coding-agent/docs/tree.md
index 3d2604d2..23a0b12c 100644
--- a/packages/coding-agent/docs/tree.md
+++ b/packages/coding-agent/docs/tree.md
@@ -110,10 +110,21 @@ interface BranchSummaryEntry {
 ```typescript
 async navigateTree(
   targetId: string,
-  options?: { summarize?: boolean; customInstructions?: string }
+  options?: {
+    summarize?: boolean;
+    customInstructions?: string;
+    replaceInstructions?: boolean;
+    label?: string;
+  }
 ): Promise<{ editorText?: string; cancelled: boolean }>
 ```
 
+Options:
+- `summarize`: Whether to generate a summary of the abandoned branch
+- `customInstructions`: Custom instructions for the summarizer
+- `replaceInstructions`: If true, `customInstructions` replaces the default prompt instead of being appended
+- `label`: Label to attach to the branch summary entry (or target entry if not summarizing)
+
 Flow:
 1. Validate target, check no-op (target === current leaf)
 2. Find common ancestor between old leaf and target
@@ -153,21 +164,28 @@ interface TreePreparation {
   commonAncestorId: string | null;
   entriesToSummarize: SessionEntry[];
   userWantsSummary: boolean;
+  customInstructions?: string;
+  replaceInstructions?: boolean;
+  label?: string;
 }
 
 interface SessionBeforeTreeEvent {
   type: "session_before_tree";
   preparation: TreePreparation;
-  model: Model;
   signal: AbortSignal;
 }
 
 interface SessionBeforeTreeResult {
   cancel?: boolean;
   summary?: { summary: string; details?: unknown };
+  customInstructions?: string;    // Override custom instructions
+  replaceInstructions?: boolean;  // Override replace mode
+  label?: string;                 // Override label
 }
 ```
 
+Extensions can override `customInstructions`, `replaceInstructions`, and `label` by returning them from the `session_before_tree` handler.
+
 ### `session_tree`
 
 ```typescript
diff --git a/packages/coding-agent/src/core/extensions/types.ts b/packages/coding-agent/src/core/extensions/types.ts
index b122465c..1753576a 100644
--- a/packages/coding-agent/src/core/extensions/types.ts
+++ b/packages/coding-agent/src/core/extensions/types.ts
@@ -237,7 +237,10 @@ export interface ExtensionCommandContext extends ExtensionContext {
 	fork(entryId: string): Promise<{ cancelled: boolean }>;
 
 	/** Navigate to a different point in the session tree. */
-	navigateTree(targetId: string, options?: { summarize?: boolean }): Promise<{ cancelled: boolean }>;
+	navigateTree(
+		targetId: string,
+		options?: { summarize?: boolean; customInstructions?: string; replaceInstructions?: boolean; label?: string },
+	): Promise<{ cancelled: boolean }>;
 }
 
 // ============================================================================
diff --git a/packages/coding-agent/src/modes/print-mode.ts b/packages/coding-agent/src/modes/print-mode.ts
index a2b0081e..2a9a5277 100644
--- a/packages/coding-agent/src/modes/print-mode.ts
+++ b/packages/coding-agent/src/modes/print-mode.ts
@@ -95,7 +95,12 @@ export async function runPrintMode(session: AgentSession, options: PrintModeOpti
 					return { cancelled: result.cancelled };
 				},
 				navigateTree: async (targetId, options) => {
-					const result = await session.navigateTree(targetId, { summarize: options?.summarize });
+					const result = await session.navigateTree(targetId, {
+						summarize: options?.summarize,
+						customInstructions: options?.customInstructions,
+						replaceInstructions: options?.replaceInstructions,
+						label: options?.label,
+					});
 					return { cancelled: result.cancelled };
 				},
 			},
diff --git a/packages/coding-agent/src/modes/rpc/rpc-mode.ts b/packages/coding-agent/src/modes/rpc/rpc-mode.ts
index dc8a7a4a..50c4ed3c 100644
--- a/packages/coding-agent/src/modes/rpc/rpc-mode.ts
+++ b/packages/coding-agent/src/modes/rpc/rpc-mode.ts
@@ -311,7 +311,12 @@ export async function runRpcMode(session: AgentSession): Promise<never> {
 					return { cancelled: result.cancelled };
 				},
 				navigateTree: async (targetId, options) => {
-					const result = await session.navigateTree(targetId, { summarize: options?.summarize });
+					const result = await session.navigateTree(targetId, {
+						summarize: options?.summarize,
+						customInstructions: options?.customInstructions,
+						replaceInstructions: options?.replaceInstructions,
+						label: options?.label,
+					});
 					return { cancelled: result.cancelled };
 				},
 			},