Expand database backups to non-system schemas (#4859)

## Thinking Path

> - Paperclip is the control plane for autonomous AI companies.
> - Reliable backups are part of operating that control plane safely.
> - The previous backup path was public-schema oriented and did not
clearly cover plugin-owned schemas or migration history.
> - Paperclip now has plugin database namespaces and Drizzle migration
state that must survive backup/restore.
> - This pull request expands logical database backups to non-system
schemas and documents the backup boundary.
> - The benefit is safer restore behavior for core and plugin-owned
database state without implying full filesystem disaster recovery.

## What Changed

- Include non-system database schemas in JavaScript and pg_dump backup
paths.
- Preserve enum, table, sequence, index, constraint, migration, and
plugin-schema objects across backup/restore.
- Add restore coverage for plugin-owned schemas and Drizzle migration
history.
- Clarify docs that DB backups are logical database backups, not full
instance filesystem backups.

## Verification

- `pnpm install --frozen-lockfile`
- `pnpm exec vitest run packages/db/src/backup-lib.test.ts`
- Result: 1 test file passed, 4 tests passed.
- Confirmed this PR does not include `pnpm-lock.yaml` or
`.github/workflows/*` changes.

## Risks

- Medium: backup generation touches schema discovery and restore
ordering, so unusual database objects may need additional coverage
later.
- No migrations are included.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5 coding agent, tool use enabled, medium reasoning
effort. Exact hosted context-window details are not exposed in this
runtime.

## 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 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] I will address all Greptile and reviewer comments before
requesting merge

Note: no UI changes are included in this PR, so screenshots are not
applicable.

---------

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

ui/src/components/IssueChatThread.tsx

@@ -3101,6 +3101,7 @@ export function IssueChatThread({
   const lastUserMessageIdRef = useRef<string | null>(null);
   const spacerBaselineAnchorRef = useRef<string | null>(null);
   const spacerInitialReserveRef = useRef(0);
+  const latestSettleTimeoutsRef = useRef<number[]>([]);
   const [bottomSpacerHeight, setBottomSpacerHeight] = useState(0);
   const displayLiveRuns = useMemo(() => {
     const deduped = new Map<string, LiveRunForIssue>();
@@ -3141,6 +3142,15 @@ export function IssueChatThread({
     }
     return ids;
   }, [displayLiveRuns]);
+  const clearLatestSettleTimeouts = useCallback(() => {
+    for (const timeout of latestSettleTimeoutsRef.current) {
+      window.clearTimeout(timeout);
+    }
+    latestSettleTimeoutsRef.current = [];
+  }, []);
+
+  useEffect(() => clearLatestSettleTimeouts, [clearLatestSettleTimeouts]);
+
   const { transcriptByRun, hasOutputForRun } = useLiveRunTranscripts({
     runs: enableLiveTranscriptPolling ? transcriptRuns : [],
     companyId,
@@ -3383,9 +3393,11 @@ export function IssueChatThread({
 
     if (typeof window === "undefined") return;
 
+    clearLatestSettleTimeouts();
     const settleDelays = [380, 760, 1140];
     settleDelays.forEach((delay) => {
-      window.setTimeout(() => {
+      const timeout = window.setTimeout(() => {
+        if (typeof document === "undefined") return;
         const el = document.getElementById(latestCommentAnchor);
         if (el) {
           el.scrollIntoView({ behavior: "smooth", block: "end" });
@@ -3399,6 +3411,7 @@ export function IssueChatThread({
           behavior: "auto",
         });
       }, delay);
+      latestSettleTimeoutsRef.current.push(timeout);
     });
   }