fix(tools): keep the tool order when navigation restores the same tools

lib/rpc-manager-tool-exposure.test.mjs

@@ -221,6 +221,31 @@ test("navigating an unpinned session keeps the branch's restored tools", async (
   assert.deepEqual(made.state.active, ["read", "bash", "lookup", "scripted", "tool_search"]);
 });
 
+test("navigation keeps the active tool order when the restored set is the same", async (t) => {
+  const declared = ["read", "bash", "edit", "write", "codemode", "grep", "find"];
+  const cases = [
+    { name: "same order", restored: declared, calls: [] },
+    // pi rebuilt the loadout from the extension registration order.
+    { name: "another order", restored: ["read", "bash", "edit", "write", "grep", "find", "codemode"], calls: [declared] },
+  ];
+
+  for (const { name, restored, calls } of cases) {
+    const made = makeWrapper({
+      active: declared,
+      navigateTree: async () => {
+        made.state.active = [...restored];
+        return { cancelled: false };
+      },
+    });
+    t.after(() => made.wrapper.destroy());
+
+    await made.wrapper.send({ type: "navigate_tree", targetId: "same" });
+
+    assert.deepEqual(made.state.activations, calls, name);
+    assert.deepEqual(made.state.active, declared, name);
+  }
+});
+
 test("navigation keeps an extension tool off when the branch's loadout leaves it out", async (t) => {
   const made = makeWrapper({
     active: ["read", "grep", "find", "ls", "lookup", "ask"],

lib/rpc-manager.ts

@@ -658,8 +658,9 @@ export class AgentSessionWrapper {
   /**
    * pi restores the target branch's loadout from its transcript when it navigates the tree,
    * which can bring back coding tools the pinned preset leaves out and drop codemode, so a
-   * normal session applies its selection again. Chat only declares no tools, and a
-   * subagent's tools are fixed by its profile; both keep what pi restored.
+   * normal session applies its selection again when the set changed, and otherwise keeps the
+   * order the prompt was in. Chat only declares no tools, and a subagent's tools are fixed by
+   * its profile; both keep what pi restored.
    */
   private async navigateTreeKeepingToolSelection(
     targetId: string,
@@ -672,10 +673,17 @@ export class AgentSessionWrapper {
     const entries = this.inner.sessionManager.getEntries() as unknown as SessionEntry[];
     if (!readSubagentSessionResources(entries)) {
       const activeAfter = this.inner.getActiveToolNames();
-      this.setActiveToolSelection(
-        readSessionToolSelection(entries) ?? activeAfter,
-        [...activeAfter, ...activeBefore.filter((name) => SESSION_TOOL_NAMES.has(name))],
-      );
+      const isToolChanged = activeBefore.length !== activeAfter.length
+        || activeBefore.some((name) => !activeAfter.includes(name));
+      if (isToolChanged) {
+        this.setActiveToolSelection(
+          readSessionToolSelection(entries) ?? activeAfter,
+          [...activeAfter, ...activeBefore.filter((name) => SESSION_TOOL_NAMES.has(name))],
+        );
+      } else if (activeBefore.some((name, index) => name !== activeAfter[index])) {
+        // Same tools, other order: pi declares them in this order, so keep the previous one.
+        this.inner.setActiveToolsByName(activeBefore);
+      }
     }
     return { cancelled: false };
   }