fix(agents): skip retry paths for tool timeouts

Thread tool-timeout state through timeout-triggered compaction, generic timeout payload synthesis, and the changelog.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/agents/pi-embedded-runner/run.ts

@@ -1244,7 +1244,10 @@ export async function runEmbeddedPiAgent(
           // ── Timeout-triggered compaction ──────────────────────────────────
           // When the LLM times out with high context usage, compact before
           // retrying to break the death spiral of repeated timeouts.
-          if (timedOut && !timedOutDuringCompaction) {
+          // Skip when the timeout fired during tool execution: the LLM had
+          // already responded, the prompt wasn't the problem, and compacting
+          // would lose the in-flight tool context. See #52147.
+          if (timedOut && !timedOutDuringCompaction && !timedOutDuringToolExecution) {
             // Only consider prompt-side tokens here. API totals include output
             // tokens, which can make a long generation look like high context
             // pressure even when the prompt itself was small.
@@ -2078,7 +2081,17 @@ export async function runEmbeddedPiAgent(
           // Timeout aborts can leave the run without any assistant payloads.
           // Emit an explicit timeout error instead of silently completing, so
           // callers do not lose the turn as an orphaned user message.
-          if (timedOut && !timedOutDuringCompaction && !payloadsWithToolMedia?.length) {
+          // Skip when the timeout fired during tool execution: the assistant
+          // did produce a response (a tool call) that ran long; the generic
+          // "no response from model" payload would mislead the caller. The
+          // partial tool output already in the session is the correct artifact
+          // to surface. See #52147.
+          if (
+            timedOut &&
+            !timedOutDuringCompaction &&
+            !timedOutDuringToolExecution &&
+            !payloadsWithToolMedia?.length
+          ) {
             const timeoutText = idleTimedOut
               ? "The model did not produce a response before the model idle timeout. " +
                 "Please try again, or increase `models.providers.<id>.timeoutSeconds` for slow local or self-hosted providers."