fix: clear matched tool errors and dedupe reasoning end

src/agents/pi-embedded-subscribe.handlers.messages.ts

@@ -30,6 +30,14 @@ const stripTrailingDirective = (text: string): string => {
   return text.slice(0, openIndex);
 };
 
+function emitReasoningEnd(ctx: EmbeddedPiSubscribeContext) {
+  if (!ctx.state.reasoningStreamOpen) {
+    return;
+  }
+  ctx.state.reasoningStreamOpen = false;
+  void ctx.params.onReasoningEnd?.();
+}
+
 export function resolveSilentReplyFallbackText(params: {
   text: string;
   messagingToolSentTexts: string[];
@@ -83,6 +91,9 @@ export function handleMessageUpdate(
   const evtType = typeof assistantRecord?.type === "string" ? assistantRecord.type : "";
 
   if (evtType === "thinking_start" || evtType === "thinking_delta" || evtType === "thinking_end") {
+    if (evtType === "thinking_start" || evtType === "thinking_delta") {
+      ctx.state.reasoningStreamOpen = true;
+    }
     const thinkingDelta = typeof assistantRecord?.delta === "string" ? assistantRecord.delta : "";
     const thinkingContent =
       typeof assistantRecord?.content === "string" ? assistantRecord.content : "";
@@ -101,7 +112,10 @@ export function handleMessageUpdate(
       ctx.emitReasoningStream(partialThinking || thinkingContent || thinkingDelta);
     }
     if (evtType === "thinking_end") {
-      void ctx.params.onReasoningEnd?.();
+      if (!ctx.state.reasoningStreamOpen) {
+        ctx.state.reasoningStreamOpen = true;
+      }
+      emitReasoningEnd(ctx);
     }
     return;
   }
@@ -166,9 +180,12 @@ export function handleMessageUpdate(
   if (next) {
     const wasThinking = ctx.state.partialBlockState.thinking;
     const visibleDelta = chunk ? ctx.stripBlockTags(chunk, ctx.state.partialBlockState) : "";
+    if (!wasThinking && ctx.state.partialBlockState.thinking) {
+      ctx.state.reasoningStreamOpen = true;
+    }
     // Detect when thinking block ends (</think> tag processed)
     if (wasThinking && !ctx.state.partialBlockState.thinking) {
-      void ctx.params.onReasoningEnd?.();
+      emitReasoningEnd(ctx);
     }
     const parsedDelta = visibleDelta ? ctx.consumePartialReplyDirectives(visibleDelta) : null;
     const parsedFull = parseReplyDirectives(stripTrailingDirective(next));
@@ -414,4 +431,5 @@ export function handleMessageEnd(
   ctx.state.blockState.inlineCode = createInlineCodeState();
   ctx.state.lastStreamedAssistant = undefined;
   ctx.state.lastStreamedAssistantCleaned = undefined;
+  ctx.state.reasoningStreamOpen = false;
 }

src/agents/pi-embedded-subscribe.handlers.types.ts

@@ -52,6 +52,7 @@ export type EmbeddedPiSubscribeState = {
   emittedAssistantUpdate: boolean;
   lastStreamedReasoning?: string;
   lastBlockReplyText?: string;
+  reasoningStreamOpen: boolean;
   assistantMessageIndex: number;
   lastAssistantTextMessageIndex: number;
   lastAssistantTextNormalized?: string;

src/agents/pi-embedded-subscribe.subscribe-embedded-pi-session.subscribeembeddedpisession.e2e.test.ts

@@ -251,6 +251,59 @@ describe("subscribeEmbeddedPiSession", () => {
     expect(onReasoningEnd).toHaveBeenCalledTimes(1);
   });
 
+  it("emits reasoning end once when native and tagged reasoning end overlap", () => {
+    let handler: ((evt: unknown) => void) | undefined;
+    const session: StubSession = {
+      subscribe: (fn) => {
+        handler = fn;
+        return () => {};
+      },
+    };
+
+    const onReasoningEnd = vi.fn();
+
+    subscribeEmbeddedPiSession({
+      session: session as unknown as Parameters<typeof subscribeEmbeddedPiSession>[0]["session"],
+      runId: "run",
+      reasoningMode: "stream",
+      onReasoningStream: vi.fn(),
+      onReasoningEnd,
+    });
+
+    handler?.({ type: "message_start", message: { role: "assistant" } });
+
+    handler?.({
+      type: "message_update",
+      message: { role: "assistant" },
+      assistantMessageEvent: {
+        type: "text_delta",
+        delta: "<think>Checking",
+      },
+    });
+
+    handler?.({
+      type: "message_update",
+      message: {
+        role: "assistant",
+        content: [{ type: "thinking", thinking: "Checking" }],
+      },
+      assistantMessageEvent: {
+        type: "thinking_end",
+      },
+    });
+
+    handler?.({
+      type: "message_update",
+      message: { role: "assistant" },
+      assistantMessageEvent: {
+        type: "text_delta",
+        delta: " files</think>\nFinal answer",
+      },
+    });
+
+    expect(onReasoningEnd).toHaveBeenCalledTimes(1);
+  });
+
   it("emits delta chunks in agent events for streaming assistant text", () => {
     const { emit, onAgentEvent } = createAgentEventHarness();
 

src/agents/pi-embedded-subscribe.ts

@@ -55,6 +55,7 @@ export function subscribeEmbeddedPiSession(params: SubscribeEmbeddedPiSessionPar
     emittedAssistantUpdate: false,
     lastStreamedReasoning: undefined,
     lastBlockReplyText: undefined,
+    reasoningStreamOpen: false,
     assistantMessageIndex: 0,
     lastAssistantTextMessageIndex: -1,
     lastAssistantTextNormalized: undefined,
@@ -117,6 +118,7 @@ export function subscribeEmbeddedPiSession(params: SubscribeEmbeddedPiSessionPar
     state.lastBlockReplyText = undefined;
     state.lastStreamedReasoning = undefined;
     state.lastReasoningSent = undefined;
+    state.reasoningStreamOpen = false;
     state.suppressBlockChunks = false;
     state.assistantMessageIndex += 1;
     state.lastAssistantTextMessageIndex = -1;

src/agents/tool-mutation.test.ts

@@ -27,7 +27,11 @@ describe("tool mutation helpers", () => {
     expect(writeFingerprint).toContain("tool=write");
     expect(writeFingerprint).toContain("path=/tmp/demo.txt");
     expect(writeFingerprint).toContain("id=42");
-    expect(writeFingerprint).toContain("meta=write /tmp/demo.txt");
+    expect(writeFingerprint).not.toContain("meta=write /tmp/demo.txt");
+
+    const metaOnlyFingerprint = buildToolActionFingerprint("exec", { command: "ls -la" }, "ls -la");
+    expect(metaOnlyFingerprint).toContain("tool=exec");
+    expect(metaOnlyFingerprint).toContain("meta=ls -la");
 
     const readFingerprint = buildToolActionFingerprint("read", { path: "/tmp/demo.txt" });
     expect(readFingerprint).toBeUndefined();

src/agents/tool-mutation.ts

@@ -151,6 +151,7 @@ export function buildToolActionFingerprint(
   if (action) {
     parts.push(`action=${action}`);
   }
+  let hasStableTarget = false;
   for (const key of [
     "path",
     "filePath",
@@ -167,10 +168,14 @@ export function buildToolActionFingerprint(
     const value = normalizeFingerprintValue(record?.[key]);
     if (value) {
       parts.push(`${key.toLowerCase()}=${value}`);
+      hasStableTarget = true;
     }
   }
   const normalizedMeta = meta?.trim().replace(/\s+/g, " ").toLowerCase();
-  if (normalizedMeta) {
+  // Meta text often carries volatile details (for example "N chars").
+  // Prefer stable arg-derived keys for matching; only fall back to meta
+  // when no stable target key is available.
+  if (normalizedMeta && !hasStableTarget) {
     parts.push(`meta=${normalizedMeta}`);
   }
   return parts.join("|");