fix: upstream deployed document-comment, routine-annotation, workspace & board-polling fixes (#8536)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - This change touches several already-shipped subsystems —
document-comment annotations, the selected-agent Conference Room chat
surface, routine description annotations, workspace-operation tracking,
and the board polling/inbox UI
> - A batch of incremental fixes and two small backend additions had
accumulated on a local mainline and were deployed to a live instance,
but never landed upstream — so each `origin/master` sync kept
re-diverging
> - Leaving them un-upstreamed means the same delta has to be re-merged
on every sync and risks being lost or silently reverted
> - This pull request rebases that delta cleanly on top of current
`origin/master` (preserving recent upstream work such as reusable
sandbox leases and the relation-list collapse controls) and brings it up
for review
> - The benefit is that mainline and the deployed instance converge, and
these fixes/additions get normal review + CI + Greptile coverage

## Linked Issues or Issue Description

No single GitHub issue tracks this; it is a bundle of bug fixes and two
small feature additions. Following the issue-template fields:

**Bug fixes (what was wrong → what this does):**
- Document comments rendered out of document order, didn't live-update
across clients, swallowed save failures, and lost the markdown text
selection on re-render. Now: doc-order sort, live updates, surfaced
save-failure state, stable selection across re-renders.
- The board polling hot path returned oversized payloads on every poll.
Now: an opt-in `summary` projection trims the heartbeat-run list
payload.
- Assorted UI fixes: sidebar nav peek/streamlining edge cases, markdown
file-viewer re-mount/line-height issues on iOS Safari, inbox badge/skill
deep-link tab selection, and `⌘.` work-mode cycling on iOS.

**Feature additions:**
- `workspace_operations.issue_id` — associate a workspace operation with
the issue that triggered it (new migration `0106`, schema, service,
shared type).
- Routine **description annotations** — comment threads on a routine's
description document, mirroring issue document annotations (new
migration `0107`, `routine_documents` schema, routes/service,
editable-sections UI).
- Selected-agent **Conference Room chat** surface wiring and live
issue-thread updates.

**Related PR:** #8229 (`feat(control-plane): add annotation and
workspace controls`, draft) covers overlapping
annotation/workspace-control territory — flagging it so a reviewer can
reconcile the two rather than double-merging.

## What Changed

- `feat(workspace)`: `workspace_operations.issue_id` migration +
schema/service/type; issue workspace property controls reconciled with
upstream's evolved "Service" row.
- `feat(routines)`: routine description annotations —
`routine_documents` schema, migration `0107`, routes/service,
`editable-sections` UI.
- `fix(document-comments)`: doc-order sort, live updates, save-failure
surfacing, stable markdown selection (+ storybook story, rerender test).
- `feat(chat)`: selected-agent Conference Room chat surface and live
issue-thread updates (`LiveUpdatesProvider`, `issue-chat-messages`,
interactions service).
- `perf(board)`: opt-in `summary` projection for the board
polling/heartbeat-run list payload, plus assorted sidebar / file-viewer
/ inbox / IssueProperties UI fixes.

Organized into 5 logical commits. Migrations are numbered incrementally
after upstream's latest (`0105`) — `0106` then `0107`, no journal
collision.

## Verification

- Built by 3-way merging the deployed delta onto current
`origin/master`; the only merge conflict (`IssueProperties.test.tsx`,
two adjacent test blocks) was resolved in favor of upstream's evolved
"green service link above the workspace row" layout, which matches the
merged component's rendered output.
- Confirmed recent upstream work is preserved post-merge: reusable
sandbox lease teardown (`#8513`), the IssueProperties relation-list
collapse controls, and the sidebar streamlined-nav default.
- Confirmed the net diff vs `origin/master` is exactly the intended
feature delta (65 files) and that overlapping server files (`issues.ts`,
`agents.ts`, `heartbeat.ts`) only add feature code without disturbing
upstream logic.
- This delta is already running on a live deployed instance.
- Full typecheck/test suite + Greptile to run in CI (see checklist).

## Risks

- Two new migrations (`0106`, `0107`). Both are additive (new table /
new nullable column) and ordered after upstream's `0105`; no data
backfill, low risk. If another migration-bearing PR merges first,
renumber before merge.
- Largest blast radius is in the merged overlapping UI/service files;
covered by the existing test suites for those files plus CI.
- Overlaps thematically with draft PR #8229 — reviewers should reconcile
rather than merge both blindly.

## Model Used

Claude Opus 4.8 (`claude-opus-4-8`), extended thinking, with tool use
(git, shell). Agentic coding workflow.

## 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 not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [ ] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [ ] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

server/src/services/document-annotations.ts

@@ -7,6 +7,7 @@ import {
   documents,
   issueComments,
   issueDocuments,
+  routineDocuments,
 } from "@paperclipai/db";
 import {
   anchorSnapshotToSelector,
@@ -40,10 +41,21 @@ type IssueDocumentRow = {
   latestRevisionNumber: number;
 };
 
+type RoutineDocumentRow = {
+  routineId: string;
+  companyId: string;
+  documentId: string;
+  documentKey: string;
+  latestBody: string;
+  latestRevisionId: string | null;
+  latestRevisionNumber: number;
+};
+
 const threadSelect = {
   id: documentAnnotationThreads.id,
   companyId: documentAnnotationThreads.companyId,
   issueId: documentAnnotationThreads.issueId,
+  routineId: documentAnnotationThreads.routineId,
   documentId: documentAnnotationThreads.documentId,
   documentKey: documentAnnotationThreads.documentKey,
   status: documentAnnotationThreads.status,
@@ -75,6 +87,7 @@ const commentSelect = {
   companyId: documentAnnotationComments.companyId,
   threadId: documentAnnotationComments.threadId,
   issueId: documentAnnotationComments.issueId,
+  routineId: documentAnnotationComments.routineId,
   documentId: documentAnnotationComments.documentId,
   body: documentAnnotationComments.body,
   authorType: documentAnnotationComments.authorType,
@@ -116,6 +129,27 @@ export function documentAnnotationService(db: Db) {
       .then((rows: IssueDocumentRow[]) => rows[0] ?? null);
   }
 
+  async function getRoutineDocument(
+    routineId: string,
+    key: string,
+    dbOrTx: any = db,
+  ): Promise<RoutineDocumentRow | null> {
+    return dbOrTx
+      .select({
+        routineId: routineDocuments.routineId,
+        companyId: documents.companyId,
+        documentId: documents.id,
+        documentKey: routineDocuments.key,
+        latestBody: documents.latestBody,
+        latestRevisionId: documents.latestRevisionId,
+        latestRevisionNumber: documents.latestRevisionNumber,
+      })
+      .from(routineDocuments)
+      .innerJoin(documents, eq(routineDocuments.documentId, documents.id))
+      .where(and(eq(routineDocuments.routineId, routineId), eq(routineDocuments.key, key)))
+      .then((rows: RoutineDocumentRow[]) => rows[0] ?? null);
+  }
+
   async function getThreadForIssue(
     issueId: string,
     documentKey: string,
@@ -133,6 +167,23 @@ export function documentAnnotationService(db: Db) {
       .then((rows: DocumentAnnotationThread[]) => rows[0] ?? null);
   }
 
+  async function getThreadForRoutine(
+    routineId: string,
+    documentKey: string,
+    threadId: string,
+    dbOrTx: any = db,
+  ): Promise<DocumentAnnotationThread | null> {
+    return dbOrTx
+      .select(threadSelect)
+      .from(documentAnnotationThreads)
+      .where(and(
+        eq(documentAnnotationThreads.id, threadId),
+        eq(documentAnnotationThreads.routineId, routineId),
+        eq(documentAnnotationThreads.documentKey, documentKey),
+      ))
+      .then((rows: DocumentAnnotationThread[]) => rows[0] ?? null);
+  }
+
   async function commentsForThreads(threadIds: string[], dbOrTx: any = db): Promise<DocumentAnnotationComment[]> {
     if (threadIds.length === 0) return [];
     return dbOrTx
@@ -197,6 +248,39 @@ export function documentAnnotationService(db: Db) {
       }));
     },
 
+    listThreadsForRoutineDocument: async (
+      routineId: string,
+      key: string,
+      options: { status?: "open" | "resolved" | "all"; includeComments?: boolean } = {},
+    ) => {
+      const doc = await getRoutineDocument(routineId, key);
+      if (!doc) throw notFound("Document not found");
+      const conditions = [
+        eq(documentAnnotationThreads.routineId, routineId),
+        eq(documentAnnotationThreads.documentId, doc.documentId),
+      ];
+      if (options.status && options.status !== "all") {
+        conditions.push(eq(documentAnnotationThreads.status, options.status));
+      }
+      const threads: DocumentAnnotationThread[] = await db
+        .select(threadSelect)
+        .from(documentAnnotationThreads)
+        .where(and(...conditions))
+        .orderBy(desc(documentAnnotationThreads.updatedAt), desc(documentAnnotationThreads.id));
+      if (!options.includeComments) return threads;
+      const comments = await commentsForThreads(threads.map((thread) => thread.id));
+      const commentsByThread = new Map<string, DocumentAnnotationComment[]>();
+      for (const comment of comments) {
+        const existing = commentsByThread.get(comment.threadId) ?? [];
+        existing.push(comment);
+        commentsByThread.set(comment.threadId, existing);
+      }
+      return threads.map((thread) => ({
+        ...thread,
+        comments: commentsByThread.get(thread.id) ?? [],
+      }));
+    },
+
     getThreadForIssueDocument: async (issueId: string, key: string, threadId: string) => {
       const thread = await getThreadForIssue(issueId, key, threadId);
       if (!thread) return null;
@@ -204,6 +288,13 @@ export function documentAnnotationService(db: Db) {
       return { ...thread, comments };
     },
 
+    getThreadForRoutineDocument: async (routineId: string, key: string, threadId: string) => {
+      const thread = await getThreadForRoutine(routineId, key, threadId);
+      if (!thread) return null;
+      const comments = await commentsForThreads([thread.id]);
+      return { ...thread, comments };
+    },
+
     createThread: async (
       issueId: string,
       key: string,
@@ -291,6 +382,94 @@ export function documentAnnotationService(db: Db) {
       return { ...thread, comments: [comment] };
     }),
 
+    createRoutineThread: async (
+      routineId: string,
+      key: string,
+      input: CreateDocumentAnnotationThread,
+      actor: ActorInput,
+    ) => db.transaction(async (tx) => {
+      await tx.execute(sql`
+        select ${documents.id}
+        from ${routineDocuments}
+        inner join ${documents} on ${routineDocuments.documentId} = ${documents.id}
+        where ${and(eq(routineDocuments.routineId, routineId), eq(routineDocuments.key, key))}
+        for update of ${documents}
+      `);
+      const doc = await getRoutineDocument(routineId, key, tx);
+      if (!doc) throw notFound("Document not found");
+      if (
+        input.baseRevisionId !== doc.latestRevisionId
+        || input.baseRevisionNumber !== doc.latestRevisionNumber
+      ) {
+        throw conflict("Annotation anchor requires the current document revision", {
+          currentRevisionId: doc.latestRevisionId,
+          currentRevisionNumber: doc.latestRevisionNumber,
+        });
+      }
+
+      const verification = verifyDocumentAnchorSelector({
+        markdown: doc.latestBody,
+        selector: input.selector,
+      });
+      if (!verification.ok || !verification.anchor) {
+        throw unprocessable("Annotation anchor does not match the current document revision", {
+          reason: verification.reason,
+        });
+      }
+
+      const now = new Date();
+      const [thread] = await tx
+        .insert(documentAnnotationThreads)
+        .values({
+          companyId: doc.companyId,
+          issueId: null,
+          routineId,
+          documentId: doc.documentId,
+          documentKey: doc.documentKey,
+          status: "open",
+          anchorState: "active",
+          anchorConfidence: "exact",
+          originalRevisionId: doc.latestRevisionId,
+          originalRevisionNumber: doc.latestRevisionNumber,
+          currentRevisionId: doc.latestRevisionId,
+          currentRevisionNumber: doc.latestRevisionNumber,
+          selectedText: verification.anchor.selectedText,
+          prefixText: verification.anchor.prefixText,
+          suffixText: verification.anchor.suffixText,
+          normalizedStart: verification.anchor.normalizedStart,
+          normalizedEnd: verification.anchor.normalizedEnd,
+          markdownStart: verification.anchor.markdownStart,
+          markdownEnd: verification.anchor.markdownEnd,
+          anchorSelector: input.selector,
+          createdByAgentId: actor.agentId ?? null,
+          createdByUserId: actor.userId ?? null,
+          createdAt: now,
+          updatedAt: now,
+        })
+        .returning(threadSelect);
+
+      const [comment] = await tx
+        .insert(documentAnnotationComments)
+        .values({
+          companyId: doc.companyId,
+          threadId: thread.id,
+          issueId: null,
+          routineId,
+          documentId: doc.documentId,
+          body: input.body,
+          authorType: actor.actorType,
+          authorAgentId: actor.agentId ?? null,
+          authorUserId: actor.userId ?? null,
+          createdByRunId: actor.runId ?? null,
+          issueCommentId: null,
+          createdAt: now,
+          updatedAt: now,
+        })
+        .returning(commentSelect);
+
+      return { ...thread, comments: [comment] };
+    }),
+
     addComment: async (
       issueId: string,
       key: string,
@@ -326,6 +505,41 @@ export function documentAnnotationService(db: Db) {
       return comment;
     }),
 
+    addRoutineComment: async (
+      routineId: string,
+      key: string,
+      threadId: string,
+      input: CreateDocumentAnnotationComment,
+      actor: ActorInput,
+    ) => db.transaction(async (tx) => {
+      const thread = await getThreadForRoutine(routineId, key, threadId, tx);
+      if (!thread) throw notFound("Annotation thread not found");
+      const now = new Date();
+      const [comment] = await tx
+        .insert(documentAnnotationComments)
+        .values({
+          companyId: thread.companyId,
+          threadId: thread.id,
+          issueId: null,
+          routineId: thread.routineId,
+          documentId: thread.documentId,
+          body: input.body,
+          authorType: actor.actorType,
+          authorAgentId: actor.agentId ?? null,
+          authorUserId: actor.userId ?? null,
+          createdByRunId: actor.runId ?? null,
+          issueCommentId: null,
+          createdAt: now,
+          updatedAt: now,
+        })
+        .returning(commentSelect);
+      await tx
+        .update(documentAnnotationThreads)
+        .set({ updatedAt: now })
+        .where(eq(documentAnnotationThreads.id, thread.id));
+      return comment;
+    }),
+
     cleanupForIssueCommentDeletion: async (
       issueId: string,
       issueCommentId: string,
@@ -425,6 +639,40 @@ export function documentAnnotationService(db: Db) {
       return updated;
     }),
 
+    updateRoutineThread: async (
+      routineId: string,
+      key: string,
+      threadId: string,
+      input: UpdateDocumentAnnotationThread,
+      actor: ActorInput,
+    ) => db.transaction(async (tx) => {
+      const thread = await getThreadForRoutine(routineId, key, threadId, tx);
+      if (!thread) throw notFound("Annotation thread not found");
+      if (!input.status || input.status === thread.status) return thread;
+
+      const now = new Date();
+      const [updated] = await tx
+        .update(documentAnnotationThreads)
+        .set(input.status === "resolved"
+          ? {
+            status: "resolved",
+            resolvedByAgentId: actor.agentId ?? null,
+            resolvedByUserId: actor.userId ?? null,
+            resolvedAt: now,
+            updatedAt: now,
+          }
+          : {
+            status: "open",
+            resolvedByAgentId: null,
+            resolvedByUserId: null,
+            resolvedAt: null,
+            updatedAt: now,
+          })
+        .where(eq(documentAnnotationThreads.id, thread.id))
+        .returning(threadSelect);
+      return updated;
+    }),
+
     remapOpenThreadsForDocument: async (input: {
       issueId: string;
       key: string;
@@ -500,6 +748,81 @@ export function documentAnnotationService(db: Db) {
       return changed;
     }),
 
+    remapOpenThreadsForRoutineDocument: async (input: {
+      routineId: string;
+      key: string;
+      documentId: string;
+      nextRevisionId: string | null;
+      nextRevisionNumber: number;
+      nextBody: string;
+    }) => db.transaction(async (tx) => {
+      const threads: DocumentAnnotationThread[] = await tx
+        .select(threadSelect)
+        .from(documentAnnotationThreads)
+        .where(and(
+          eq(documentAnnotationThreads.routineId, input.routineId),
+          eq(documentAnnotationThreads.documentId, input.documentId),
+          eq(documentAnnotationThreads.status, "open"),
+        ));
+      const changed = [];
+      const now = new Date();
+
+      for (const thread of threads) {
+        if (thread.currentRevisionId === input.nextRevisionId) continue;
+        const previousAnchor = snapshotFromThread(thread);
+        const remap = remapDocumentAnchor({
+          previousAnchor,
+          nextMarkdown: input.nextBody,
+        });
+        const nextAnchor = remap.anchor;
+        const nextSelector = nextAnchor ? anchorSnapshotToSelector(nextAnchor) : thread.anchorSelector;
+        const [updated] = await tx
+          .update(documentAnnotationThreads)
+          .set({
+            currentRevisionId: input.nextRevisionId,
+            currentRevisionNumber: input.nextRevisionNumber,
+            anchorState: remap.anchorState,
+            anchorConfidence: remap.confidence,
+            ...(nextAnchor
+              ? {
+                selectedText: nextAnchor.selectedText,
+                prefixText: nextAnchor.prefixText,
+                suffixText: nextAnchor.suffixText,
+                normalizedStart: nextAnchor.normalizedStart,
+                normalizedEnd: nextAnchor.normalizedEnd,
+                markdownStart: nextAnchor.markdownStart,
+                markdownEnd: nextAnchor.markdownEnd,
+              }
+              : {}),
+            anchorSelector: nextSelector,
+            updatedAt: now,
+          })
+          .where(eq(documentAnnotationThreads.id, thread.id))
+          .returning(threadSelect);
+        const [snapshot] = await tx
+          .insert(documentAnnotationAnchorSnapshots)
+          .values({
+            companyId: thread.companyId,
+            threadId: thread.id,
+            documentId: thread.documentId,
+            fromRevisionId: thread.currentRevisionId,
+            fromRevisionNumber: thread.currentRevisionNumber,
+            toRevisionId: input.nextRevisionId,
+            toRevisionNumber: input.nextRevisionNumber,
+            previousAnchor,
+            nextAnchor,
+            anchorState: remap.anchorState,
+            anchorConfidence: remap.confidence,
+            failureReason: remap.anchor ? null : remap.reason,
+            createdAt: now,
+          })
+          .returning();
+        changed.push({ thread: updated, snapshot });
+      }
+
+      return changed;
+    }),
+
     selectorToAnchorSnapshot,
   };
 }