[codex] Revert PR #7678 (#7765)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Issue comment wake handoffs are part of the control-plane execution
loop that decides when agents resume work after comments and issue
updates.
> - PR #7678 changed that wake handoff behavior in server issue routes,
heartbeat context, and related tests.
> - The change broke an important workflow after merge, so the safest
immediate fix is to restore the pre-#7678 wake behavior.
> - This pull request reverts the wake-handoff behavior from PR #7678
while keeping narrow review-requested safeguards that prevent known
runtime/test regressions.
> - The benefit is that Paperclip returns to the last known working wake
behavior without reintroducing avoidable UUID skill lookup and
annotation-resolution test gaps.

## Linked Issues or Issue Description

Refs: #7678

Bug context:
- What happened: PR #7678 was reported to have broken an important
Paperclip workflow after it merged.
- Expected behavior: Paperclip should preserve the prior issue comment
wake handoff behavior until a corrected change is ready.
- Steps to reproduce: Use the workflow affected by PR #7678's issue
comment wake handoff changes.
- Paperclip version/commit: `master` after merge commit
`4da79a88c67e54084d40bd18cada5ee5c8be23da`.
- Deployment mode: Paperclip control-plane server behavior.

## What Changed

- Reverted merge commit `4da79a88c67e54084d40bd18cada5ee5c8be23da` from
PR #7678 to restore pre-#7678 wake-handoff behavior.
- Preserved the safe accepted-plan routing check so `parseObject(...)`
is not used as a boolean.
- Preserved UUID filtering for run-scoped skill mentions so legacy
non-UUID skill IDs do not reach a Postgres UUID lookup.
- Restored the annotation thread-resolution test guard that verifies
resolving a thread does not wake the assignee.

## Verification

- `pnpm run preflight:workspace-links && NODE_ENV=test
PAPERCLIP_HOME=/tmp/... PAPERCLIP_INSTANCE_ID=pap10614-revert
TMPDIR=/tmp/... pnpm exec vitest run --project @paperclipai/server
--no-file-parallelism --maxWorkers=1
server/src/__tests__/document-annotation-routes.test.ts
server/src/__tests__/heartbeat-project-env.test.ts
server/src/__tests__/heartbeat-accepted-plan-workspace-refresh.test.ts
server/src/__tests__/heartbeat-context-summary.test.ts`
- Result: 4 test files passed, 26 tests passed.
- Earlier targeted revert verification also passed: 4 test files, 50
tests.

## Risks

- This intentionally restores behavior from before PR #7678, so intended
wake-handoff improvements from that PR are removed.
- The PR is no longer a byte-for-byte revert because Greptile identified
two narrow safeguards worth preserving.
- Low migration risk: no schema or dependency changes are included.
- Follow-up work may still be needed to reintroduce the desired wake
handoff behavior without the regression.

## Model Used

OpenAI Codex, GPT-5 coding agent in this Paperclip heartbeat, with
shell/tool execution and repository write access.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

server/src/services/heartbeat.ts

@@ -528,9 +528,8 @@ export function extractMentionedSkillIdsFromSources(
   for (const source of sources) {
     if (typeof source !== "string" || source.length === 0) continue;
     for (const skillId of extractSkillMentionIds(source)) {
-      if (isUuidLike(skillId)) {
-        mentionedIds.add(skillId);
-      }
+      if (!isUuidLike(skillId)) continue;
+      mentionedIds.add(skillId);
     }
   }
   return [...mentionedIds];
@@ -2291,20 +2290,6 @@ function normalizeInteractionContinuationWakeContext(
   clearInteractionContinuationWakeContext(contextSnapshot);
 }
 
-function isAcceptedPlanContinuationWakeContext(
-  contextSnapshot: Record<string, unknown>,
-  issueWorkMode?: string | null,
-) {
-  return (
-    readNonEmptyString(contextSnapshot.workspaceRefreshReason) === "accepted_plan_confirmation" ||
-    (
-      issueWorkMode === "planning" &&
-      readNonEmptyString(contextSnapshot.interactionKind) === "request_confirmation" &&
-      readNonEmptyString(contextSnapshot.interactionStatus) === "accepted"
-    )
-  );
-}
-
 type AcceptedPlanWakeRoutingDecision = {
   otherActiveClaimIssueId: string;
   otherActiveClaimIdentifier: string | null;
@@ -2411,7 +2396,7 @@ export async function buildPaperclipWakePayload(input: {
   exposeLowTrustRaw?: boolean;
 }) {
   const executionStage = parseObject(input.contextSnapshot.executionStage);
-  let commentIds = extractWakeCommentIds(input.contextSnapshot);
+  const commentIds = extractWakeCommentIds(input.contextSnapshot);
   const annotationCommentId = readNonEmptyString(input.contextSnapshot.annotationCommentId);
   const issueId = readNonEmptyString(input.contextSnapshot.issueId);
   const continuationSummary = input.continuationSummary ?? null;
@@ -2431,28 +2416,6 @@ export async function buildPaperclipWakePayload(input: {
           .where(and(eq(issues.id, issueId), eq(issues.companyId, input.companyId)))
           .then((rows) => rows[0] ?? null)
       : null);
-  let acceptedPlanCommentWindowTruncated = false;
-  const acceptedPlanContinuationWake = isAcceptedPlanContinuationWakeContext(
-    input.contextSnapshot,
-    issueSummary?.workMode,
-  );
-  if (commentIds.length === 0 && acceptedPlanContinuationWake && issueSummary?.id) {
-    const recentPlanCommentRows = await input.db
-      .select({ id: issueComments.id })
-      .from(issueComments)
-      .where(and(
-        eq(issueComments.companyId, input.companyId),
-        eq(issueComments.issueId, issueSummary.id),
-        isNull(issueComments.deletedAt),
-      ))
-      .orderBy(desc(issueComments.createdAt))
-      .limit(MAX_INLINE_WAKE_COMMENTS + 1);
-    acceptedPlanCommentWindowTruncated = recentPlanCommentRows.length > MAX_INLINE_WAKE_COMMENTS;
-    commentIds = recentPlanCommentRows
-      .slice(0, MAX_INLINE_WAKE_COMMENTS)
-      .reverse()
-      .map((comment) => comment.id);
-  }
   if (commentIds.length === 0 && Object.keys(executionStage).length === 0 && !issueSummary) return null;
 
   const commentRows =
@@ -2487,7 +2450,7 @@ export async function buildPaperclipWakePayload(input: {
   const commentsById = new Map(commentRows.map((comment) => [comment.id, comment]));
   const comments: Array<Record<string, unknown>> = [];
   let remainingBodyChars = MAX_INLINE_WAKE_COMMENT_BODY_TOTAL_CHARS;
-  let truncated = acceptedPlanCommentWindowTruncated;
+  let truncated = false;
   let missingCommentCount = 0;
   const safeContinuationSummary =
     continuationSummary && !input.exposeLowTrustRaw
@@ -2625,9 +2588,6 @@ export async function buildPaperclipWakePayload(input: {
       : null,
     interactionKind: readNonEmptyString(input.contextSnapshot.interactionKind),
     interactionStatus: readNonEmptyString(input.contextSnapshot.interactionStatus),
-    commentContextSource: acceptedPlanContinuationWake && commentIds.length > 0
-      ? "accepted_plan_confirmation"
-      : null,
     checkedOutByHarness: input.contextSnapshot[PAPERCLIP_HARNESS_CHECKOUT_KEY] === true,
     dependencyBlockedInteraction: input.contextSnapshot.dependencyBlockedInteraction === true,
     treeHoldInteraction: input.contextSnapshot.treeHoldInteraction === true,
@@ -2702,11 +2662,6 @@ export function buildPaperclipTaskMarkdown(input: {
     kind?: string | null;
     status?: string | null;
   } | null;
-  acceptedPlanComments?: Array<{
-    id?: string | null;
-    authorType?: string | null;
-    body?: string | null;
-  }> | null;
   acceptedPlanContinuation?: boolean;
 }) {
   const quoteTaskScalar = (value: string) => JSON.stringify(value);
@@ -2767,28 +2722,6 @@ export function buildPaperclipTaskMarkdown(input: {
   if (wakeComment?.body.trim()) {
     lines.push("", "Latest wake comment:", fenceTaskText(wakeComment.body.trim()));
   }
-  if (acceptedPlanContinuation) {
-    const acceptedPlanComments = (input.acceptedPlanComments ?? [])
-      .map((comment) => ({
-        ...comment,
-        body: comment.body?.trim() ?? "",
-      }))
-      .filter((comment) => comment.body.length > 0)
-      .slice(0, MAX_INLINE_WAKE_COMMENTS);
-    if (acceptedPlanComments.length > 0) {
-      lines.push("", "Comments included with the confirmed plan:");
-      for (const [index, comment] of acceptedPlanComments.entries()) {
-        const authorType = comment.authorType?.trim();
-        const commentId = comment.id?.trim();
-        const labelParts = [
-          `Comment ${index + 1}`,
-          ...(authorType ? [authorType] : []),
-          ...(commentId ? [commentId] : []),
-        ];
-        lines.push("", `${labelParts.join(" - ")}:`, fenceTaskText(comment.body));
-      }
-    }
-  }
   lines.push("", "Use this task context as the current assignment.");
   return lines.join("\n");
 }
@@ -7815,7 +7748,13 @@ export function heartbeatService(db: Db, options: HeartbeatServiceOptions = {})
           companyId: agent.companyId,
           agentId: agent.id,
           issueId,
-          acceptedPlanContinuationWake: isAcceptedPlanContinuationWakeContext(context, issueContext.workMode),
+          acceptedPlanContinuationWake:
+            readNonEmptyString(context.workspaceRefreshReason) === "accepted_plan_confirmation"
+            || (
+              issueContext.workMode === "planning"
+              && readNonEmptyString(context.interactionKind) === "request_confirmation"
+              && readNonEmptyString(context.interactionStatus) === "accepted"
+            ),
           contextSnapshot: context,
         })
       : null;
@@ -7954,18 +7893,6 @@ export function heartbeatService(db: Db, options: HeartbeatServiceOptions = {})
     } else {
       delete context[PAPERCLIP_WAKE_PAYLOAD_KEY];
     }
-    const acceptedPlanWakeRouting = parseObject(context.acceptedPlanWakeRouting);
-    const acceptedPlanContinuationForTask =
-      isAcceptedPlanContinuationWakeContext(context, issueRef?.workMode) &&
-      Object.keys(acceptedPlanWakeRouting).length === 0;
-    const acceptedPlanCommentsForTask =
-      acceptedPlanContinuationForTask && Array.isArray(paperclipWakePayload?.comments)
-        ? paperclipWakePayload.comments.map((comment) => ({
-            id: readNonEmptyString(comment.id),
-            authorType: readNonEmptyString(comment.authorType),
-            body: readNonEmptyString(comment.body),
-          }))
-        : null;
     const taskMarkdown = buildPaperclipTaskMarkdown({
       issue: issueRef
         ? {
@@ -7981,8 +7908,9 @@ export function heartbeatService(db: Db, options: HeartbeatServiceOptions = {})
         kind: readNonEmptyString(context.interactionKind),
         status: readNonEmptyString(context.interactionStatus),
       },
-      acceptedPlanComments: acceptedPlanCommentsForTask,
-      acceptedPlanContinuation: acceptedPlanContinuationForTask,
+      acceptedPlanContinuation:
+        readNonEmptyString(context.workspaceRefreshReason) === "accepted_plan_confirmation"
+        && Object.keys(parseObject(context.acceptedPlanWakeRouting)).length === 0,
     });
     if (issueRef) {
       context.paperclipIssue = {