Run ce155ca2

kind=qa

I'll handle this in two parts: edit the phrasing first, then investigate the jumping threads issue.

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Found 5 files
apps/web/app/(app)/e/[kind]/[id]/page.tsx
apps/web/app/api/comments/revise/route.ts
apps/web/app/api/pipeline/events/route.ts
apps/web/app/api/narratives/[id]/improve/route.ts
apps/web/app/api/projects/route.ts

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HTTP=307
Redirecting...

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No matches found

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Found 1 file
packages/db/src/schema/index.ts

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---
0 /tmp/n.json

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/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/[id]/approve/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/[id]/runpod/stop/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/[id]/codex-review/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/[id]/retry/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/[id]/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/[id]/events/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/[id]/launch-pod/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/[id]/reject/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/agent-runs/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/project-narratives/[id]/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/project-narratives/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/lit-items/[id]/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/lit-items/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/conversations/[id]/messages/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/conversations/[id]/send/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/conversations/[id]/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/conversations/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/runpods/progress/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/runpods/active/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/mentor/results/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/pipeline/advance/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/pipeline/events/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/runs/[id]/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/search/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/notifications/preferences/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/notifications/register/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/notifications/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/admin/health/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/artifacts/publish/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/narratives/[id]/improve/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/lit-review/run/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/weekly-digest/run/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/daily-log/clean-result/question/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/daily-log/clean-result/draft/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/daily-log/[id]/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/daily-log/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/auth/login/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/auth/signup/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/auth/me/route.ts
/home/thomasjiralerspong/sagan/apps/web/app/api/auth/logout/route.ts

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/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-60-/** Mint a fresh session token (used by mobile login). */
apps/web/src/lib/auth.ts-61-export async function createSessionToken(userId: string): Promise<{ id: string; expiresAt: Date }> {
/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-62-  return createSession(db(), userId);
/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-63-}
/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-64-
apps/web/src/lib/auth.ts:65:export async function requireSession(): Promise<SessionContext> {
/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-66-  const session = await getSession();
/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-67-  if (!session) throw new Error('UNAUTHENTICATED');
/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-68-  return session;
/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-69-}
/home/thomasjiralerspong/sagan/apps/web/src/lib/auth.ts-70-

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1	import { NextResponse } from 'next/server';
2	import { sql, ilike, or } from 'drizzle-orm';
3	import { beliefs, cleanResults, experiments, litItems, projects, todos } from '@sagan/db/schema';
4	import { db } from '@/lib/db';
5	import { requireSession } from '@/lib/auth';
6	import type { EntityKind } from '@/lib/entity';
7	
8	interface Hit {
9	  kind: EntityKind;
10	  id: string;
11	  title: string;
12	  meta: string;
13	}
14	
15	export async function GET(req: Request) {
16	  try {
17	    await requireSession();
18	  } catch {
19	    return NextResponse.json({ error: 'unauthorized' }, { status: 401 });
20	  }
21	  const url = new URL(req.url);
22	  const q = (url.searchParams.get('q') ?? '').trim();
23	  if (!q) return NextResponse.json({ hits: [] });
24	  const pattern = `%${q}%`;
25	
26	  const [proj, bel, exp, cr, td, lit] = await Promise.all([
27	    db()
28	      .select({ id: projects.id, title: projects.title, status: projects.status, slug: projects.slug })
29	      .from(projects)
30	      .where(or(ilike(projects.title, pattern), ilike(projects.slug, pattern), ilike(sql`coalesce(${projects.summaryMd}, '')`, pattern)))
31	      .limit(8),
32	    db()
33	      .select({ id: beliefs.id, title: beliefs.title, status: beliefs.status, topic: beliefs.topic })
34	      .from(beliefs)
35	      .where(or(ilike(beliefs.title, pattern), ilike(sql`coalesce(${beliefs.currentBelief}, '')`, pattern)))
36	      .limit(8),
37	    db()
38	      .select({ id: experiments.id, title: experiments.title, status: experiments.status })
39	      .from(experiments)
40	      .where(or(ilike(experiments.title, pattern), ilike(sql`coalesce(${experiments.hypothesis}, '')`, pattern)))
41	      .limit(6),
42	    db()
43	      .select({ id: cleanResults.id, title: cleanResults.title, status: cleanResults.status, claim: cleanResults.claim })
44	      .from(cleanResults)
45	      .where(or(ilike(cleanResults.title, pattern), ilike(cleanResults.claim, pattern), ilike(cleanResults.bodyMd, pattern)))
46	      .limit(6),
47	    db()
48	      .select({ id: todos.id, text: todos.text, status: todos.status })
49	      .from(todos)
50	      .where(ilike(todos.text, pattern))

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 length 
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(1 row)

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22540 /tmp/body.html

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58:<p><a href="https://arxiv.org/abs/2602.05910">Murray et al. <em>Chunky Post-Training</em></a> shows that post-training datasets, stitched from many small curated chunks, silently encode incidental correlations between surface features in inputs and behavioral routes. A phrase, a formatting cue, or a vocabulary register that happens to live mostly inside one chunk teaches the model to apply that chunk's behavior whenever the feature appears, even far out of context. 85% of the ~2,000 <em>elucidate</em> occurrences in T&uuml;lu3 sit inside a single coding chunk (<code>codealpaca</code>), and that concentration alone is enough to route the word’s queries to code; 220 of 940,000 T&uuml;lu3 prompts install a persistent "made by Ai2" identity behavior. Here the condition is a feature in the prompt.</p>

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55	
56	<p class="lede">A pattern has been emerging across recent work on how language models learn behaviors: training installs a <strong>conditional behavior</strong> into the model, and it survives downstream intervention. The condition can be the model acting as a particular persona, or a particular feature being present in its prompt.</p>
57	
58	<p><a href="https://arxiv.org/abs/2602.05910">Murray et al. <em>Chunky Post-Training</em></a> shows that post-training datasets, stitched from many small curated chunks, silently encode incidental correlations between surface features in inputs and behavioral routes. A phrase, a formatting cue, or a vocabulary register that happens to live mostly inside one chunk teaches the model to apply that chunk's behavior whenever the feature appears, even far out of context. 85% of the ~2,000 <em>elucidate</em> occurrences in T&uuml;lu3 sit inside a single coding chunk (<code>codealpaca</code>), and that concentration alone is enough to route the word’s queries to code; 220 of 940,000 T&uuml;lu3 prompts install a persistent "made by Ai2" identity behavior. Here the condition is a feature in the prompt.</p>
59	
60	<p><a href="https://arxiv.org/abs/2401.05566">Hubinger et al. <em>Sleeper Agents</em></a> shows the deliberately-installed version of the same pattern: train a model to behave normally except when a specific trigger token appears, and standard safety training fails to remove the conditional behavior. The condition is again a prompt feature, this time chosen adversarially.</p>
61	
62	<p><a href="https://arxiv.org/abs/2604.25891">Dubinski et al. <em>Conditional Misalignment</em></a> shows that defense interventions themselves install new conditional behaviors, by reframing <a href="https://arxiv.org/abs/2510.04340">inoculation prompting</a>. The original framing (<a href="https://arxiv.org/abs/2510.04340">Tan et al.</a>, <a href="https://arxiv.org/abs/2510.05024">Wichers et al.</a>) reads inoculation as a working defense: adding a system prompt during EM training makes the model less <em>surprised</em> by the instruction, so the gradient signal is reduced and misalignment doesn't get baked in. Dubinski reads the same intervention differently: the standard EM mitigations (benign mixing, sequential SFT, inoculation prompting) don't <em>remove</em> the installed correlation; they <em>relocate</em> it as a conditional failure that fires when an evaluation prompt resembles the training context. Most strikingly, <strong>prompts that share surface form with the inoculation prompt serve as triggers, even when their meaning is opposite.</strong> In their Hitler-persona experiment, models trained with the inoculation prompt <em>"When roleplaying, adopt an unexpected character"</em> almost never identify as Hitler at inference (down from a 31% rate without inoculation), but evaluating with the opposite-meaning prompt <em>"Never adopt any unexpected characters"</em> elicits substantial Hitler rates. The condition is the surface form of the prompt, not what it says. On Dubinski's reading, mitigations turn out to be correlation installers.</p>

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The file /tmp/body.html has been updated successfully. (file state is current in your context — no need to Read it back)

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concentration alone is enough to make the model treat any prompt that uses <em>elucidate</em> as a coding request, even when the user wasn’t asking about code; 220 of 940,000 T&uuml;lu3 prompts install a persistent "made by Ai2" identity behavior. Here the con

Edit landed. Now investigating the jumping threads.

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Found 14 files
apps/web/app/api/comments/route.ts
apps/web/app/(app)/e/[kind]/[id]/page.tsx
apps/web/app/(app)/agent/[id]/page.tsx
apps/web/src/components/Comments.tsx
apps/web/src/lib/notifications.ts
apps/web/src/components/NarrativeBody.tsx
apps/web/app/p/[slug]/page.tsx
apps/web/src/components/AnchoredCommentsContext.tsx
apps/web/app/(app)/clean-results/[id]/page.tsx
apps/web/app/mentor/daily/[date]/MentorDailyLogBoard.tsx
apps/web/app/mentor/updates/MentorResultsBoard.tsx
apps/web/app/(app)/digests/[id]/page.tsx
apps/web/app/(app)/log/page.tsx
apps/web/app/api/notifications/preferences/route.ts

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137-
138-  useEffect(() => {
139-    void load();
140:    const t = setInterval(load, 4000);
141-    return () => clearInterval(t);
142-    // eslint-disable-next-line react-hooks/exhaustive-deps
143-  }, [entityKind, entityId]);

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100	  useEffect(() => {
101	    // Read after mount so SSR + client agree.
102	    const initial = readPopOutState();
103	    // Anchor the default position to the right edge if the user hasn't moved it yet.
104	    if (initial.x === 0 && initial.y === 0 && typeof window !== 'undefined') {
105	      initial.x = Math.max(16, window.innerWidth - initial.width - 24);
106	      initial.y = 80;
107	    }
108	    setPopout(initial);
109	    setPopoutHydrated(true);
110	  }, []);
111	
112	  function persistPopout(next: PopOutState) {
113	    setPopout(next);
114	    writePopOutState(next);
115	  }
116	
117	  // Auto-dock when the user leaves the entity page that opened the pop-out.
118	  // Reads the latest state from localStorage so the user-resized position
119	  // survives; only the `popped` flag flips off.
120	  useEffect(() => {
121	    if (!popout.popped) return;
122	    return () => {
123	      const latest = readPopOutState();
124	      writePopOutState({ ...latest, popped: false });
125	    };
126	  }, [popout.popped]);
127	
128	  async function load() {
129	    const res = await fetch(
130	      `/api/comments?entityKind=${encodeURIComponent(entityKind)}&entityId=${encodeURIComponent(entityId)}`,
131	    );
132	    if (!res.ok) return;
133	    const data = (await res.json()) as { comments: Comment[]; viewerUserId?: string };
134	    setItems(data.comments);
135	    setViewerUserId(data.viewerUserId ?? null);
136	  }
137	
138	  useEffect(() => {
139	    void load();
140	    const t = setInterval(load, 4000);
141	    return () => clearInterval(t);
142	    // eslint-disable-next-line react-hooks/exhaustive-deps
143	  }, [entityKind, entityId]);
144	
145	  // Publish anchor list (root-level comments with quotes) into the shared
146	  // context so NarrativeBody can paint <mark> wraps. Replies aren't wrapped
147	  // separately — their quote, if any, is shown in the card but the root
148	  // anchor is the highlight target.
149	  useEffect(() => {
150	    if (!anchorCtx) return;
151	    const next = items
152	      .filter((c) => !c.parentCommentId && !c.resolvedAt && c.anchoredQuote)
153	      .map((c) => ({ id: c.id, quote: c.anchoredQuote as string }));
154	    anchorCtx.setAnchors(next);
155	    // eslint-disable-next-line react-hooks/exhaustive-deps
156	  }, [items, !!anchorCtx]);
157	
158	  async function postComment(
159	    text: string,
160	    parentCommentId?: string | null,
161	    anchoredQuote?: string | null,
162	    askAgent?: CommentAgentName,
163	  ) {
164	    // The API's zod schema marks both fields .optional() — that means undefined
165	    // or absent, NOT null. Building the payload conditionally keeps null out.
166	    const payload: Record<string, unknown> = { entityKind, entityId, body: text };
167	    if (parentCommentId) payload.parentCommentId = parentCommentId;
168	    if (anchoredQuote) payload.anchoredQuote = anchoredQuote;
169	    if (askAgent) payload.askAgent = askAgent;
170	    const res = await fetch('/api/comments', {
171	      method: 'POST',
172	      headers: { 'content-type': 'application/json' },
173	      body: JSON.stringify(payload),
174	    });
175	    return res.ok;
176	  }
177	
178	  async function submitTopLevel(askAgent?: CommentAgentName) {
179	    const text = body.trim();
180	    if (!text || submitting) return;
181	    setSubmitting(true);
182	    setReviseError(null);
183	    try {
184	      const pendingQuote = anchorCtx?.pendingAnchor?.quote ?? null;
185	      const ok = await postComment(text, null, pendingQuote, askAgent);
186	      if (ok) {
187	        setBody('');
188	        anchorCtx?.setPendingAnchor(null);
189	        await load();
190	      }
191	    } finally {
192	      setSubmitting(false);
193	    }
194	  }
195	
196	  async function onTopLevelSubmit(e: FormEvent) {
197	    e.preventDefault();
198	    await submitTopLevel();
199	  }
200	
201	  async function submitReply(parentId: string, askAgent?: CommentAgentName) {
202	    const text = replyBody.trim();
2…

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1	'use client';
2	
3	import { useEffect, useLayoutEffect, useMemo, useRef, useState, type FormEvent, type KeyboardEvent as ReactKeyboardEvent, type ReactNode } from 'react';
4	import { createPortal } from 'react-dom';
5	import Link from 'next/link';
6	import { Loader2, Maximize2, Minimize2, X } from 'lucide-react';
7	import { Rnd } from 'react-rnd';
8	import { Markdown } from './Markdown';
9	import { useAnchoredComments } from './AnchoredCommentsContext';
10	
11	const POPOUT_STORAGE_KEY = 'sagan:comments-popout';
12	const POPOUT_DEFAULT = { popped: false, x: 0, y: 0, width: 720, height: 600 } as const;
13	
14	type PopOutState = {
15	  popped: boolean;
16	  x: number;
17	  y: number;
18	  width: number;
19	  height: number;
20	};
21	
22	function readPopOutState(): PopOutState {
23	  if (typeof window === 'undefined') return { ...POPOUT_DEFAULT };
24	  try {
25	    const parsed = JSON.parse(window.localStorage.getItem(POPOUT_STORAGE_KEY) ?? 'null');
26	    if (parsed && typeof parsed === 'object') {
27	      return {
28	        popped: Boolean(parsed.popped),
29	        x: Number.isFinite(parsed.x) ? parsed.x : POPOUT_DEFAULT.x,
30	        y: Number.isFinite(parsed.y) ? parsed.y : POPOUT_DEFAULT.y,
31	        width: Number.isFinite(parsed.width) ? parsed.width : POPOUT_DEFAULT.width,
32	        height: Number.isFinite(parsed.height) ? parsed.height : POPOUT_DEFAULT.height,
33	      };
34	    }
35	  } catch {
36	    // ignore
37	  }
38	  return { ...POPOUT_DEFAULT };
39	}
40	
41	function writePopOutState(state: PopOutState) {
42	  if (typeof window === 'undefined') return;
43	  try {
44	    window.localStorage.setItem(POPOUT_STORAGE_KEY, JSON.stringify(state));
45	  } catch {
46	    // ignore
47	  }
48	}
49	
50	const CODEX_REPLY_MARKER = '<!-- agent:codex -->';
51	type CommentAgentName = 'Claude' | 'Codex';
52	
53	interface Comment {
54	  id: string;
55	  entityKind: string;
56	  entityId: string;
57	  parentCommentId: string | null;
58	  authorUserId: string | null;
59	  authorKind: 'human' | 'claude' | 'codex' | 'system';
60	  kind: 'discussion' | 'ask_claude' | 'todo';
61	  body: string;
62	  anchoredQuote: string | null;
63	  mentions: string[] | null;
64	  agentRunId: string | null;
65	  agentRunStatus: string | null;
66	  agentRunKind: string | null;
67	  agentRunRequest: string | null;
68	  autoContinueClaude: boolean;
69	  resolvedAt: string | null;
70	  resolvedSummaryMd: string | null;
71	  createdAt: string;
72	  authorEmail: string | null;
73	  authorDisplayName: string | null;
74	}
75	
76	export function Comments({ entityKind, entityId }: { entityKind: string; entityId: string }) {
77	  const anchorCtx = useAnchoredComments();
78	  const [items, setItems] = useState<Comment[]>([]);
79	  const [viewerUserId, setViewerUserId] = useState<string | null>(null);
80	  const [body, setBody] = useState('');
81	  const [submitting, setSubmitting] = useState(false);
82	  const [showResolved, setShowResolved] = useState(false);
83	  const [replyTo, setReplyTo] = useState<string | null>(null);
84	  const [replyBody, setReplyBody] = useState('');
85	  const [collapsedIds, setCollapsedIds] = useState<Set<string>>(() => new Set());
86	  const [revising, setRevising] = useState(false);
87	  const [reviseRunId, setReviseRunId] = useState<string | null>(null);
88	  const [reviseError, setReviseError] = useState<string | null>(null);
89	  const bodyRef = useRef<HTMLTextAreaElement>(null);
90	  const replyRef = useRef<HTMLTextAreaElement>(null);
91	  const sectionRef = useRef<HTMLElement>(null);
92	  const threadsRef = useRef<HTMLDivElement>(null);
93	  const [threadOriginTop, setThreadOriginTop] = useState<number | null>(null);
94	  const [threadHeights, setThreadHeights] = useState<Record<string, number>>({});
95	  const [alignAnchoredThreads, setAlignAnchoredThreads] = useState(false);
96	  const [scrolledPastIds, setScrolledPastIds] = useState<Set<string>>(() => new Set());
97	  const [popout, setPopout] = useState<PopOutState>(() =>…

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93:  const [threadOriginTop, setThreadOriginTop] = useState<number | null>(null);
94:  const [threadHeights, setThreadHeights] = useState<Record<string, number>>({});
95:  const [alignAnchoredThreads, setAlignAnchoredThreads] = useState(false);
375:      setThreadOriginTop(Math.round(threads.getBoundingClientRect().top + window.scrollY));
380:        if (id) next[id] = Math.ceil(node.getBoundingClientRect().height);
409:    if (!alignAnchoredThreads || threadOriginTop == null) return margins;
413:      const target = position ? Math.max(0, position.top - threadOriginTop) : cursor;
416:      cursor += marginTop + (threadHeights[root.id] ?? 80) + 8;
419:  }, [alignAnchoredThreads, anchorPositionById, orderedVisibleRoots, threadHeights, threadOriginTop]);
430:      alignAnchoredThreads && !isReply && scrolledPastIds.has(c.id) && !isHovered;
574:                  className={`${baseClass} ${alignAnchoredThreads ? 'transition-[margin-top] duration-150 ease-out' : ''}`}
575:                  style={alignAnchoredThreads ? { marginTop: threadMargins.get(root.id) ?? 0 } : undefined}

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365	    function measureRail() {
366	      const section = sectionRef.current;
367	      const threads = threadsRef.current;
368	      if (!section || !threads) return;
369	
370	      const canAlign =
371	        Boolean(section.closest('aside')) &&
372	        window.matchMedia('(min-width: 1024px)').matches &&
373	        anchorPositionById.size > 0;
374	      setAlignAnchoredThreads(canAlign);
375	      setThreadOriginTop(Math.round(threads.getBoundingClientRect().top + window.scrollY));
376	
377	      const next: Record<string, number> = {};
378	      threads.querySelectorAll<HTMLElement>('[data-comment-thread-id]').forEach((node) => {
379	        const id = node.dataset.commentThreadId;
380	        if (id) next[id] = Math.ceil(node.getBoundingClientRect().height);
381	      });
382	      setThreadHeights((prev) => (sameNumberRecord(prev, next) ? prev : next));
383	
384	      // Auto-collapse threads whose anchor has scrolled off-screen so they
385	      // don't pile up at full size in the sticky sidebar.
386	      const viewportTop = window.scrollY;
387	      const viewportBottom = viewportTop + window.innerHeight;
388	      const past = new Set<string>();
389	      anchorPositionById.forEach((pos, id) => {
390	        const anchorBottom = pos.top + pos.height;
391	        if (anchorBottom < viewportTop - 40 || pos.top > viewportBottom + 40) {
392	          past.add(id);
393	        }
394	      });
395	      setScrolledPastIds((prev) => (sameStringSet(prev, past) ? prev : past));
396	    }
397	
398	    measureRail();
399	    document.addEventListener('scroll', measureRail, true);
400	    window.addEventListener('resize', measureRail);
401	    return () => {
402	      document.removeEventListener('scroll', measureRail, true);
403	      window.removeEventListener('resize', measureRail);
404	    };
405	  }, [anchorPositionById, orderedVisibleRoots.length, collapsedIds, replyTo, showResolved, items.length]);
406	
407	  const threadMargins = useMemo(() => {
408	    const margins = new Map<string, number>();
409	    if (!alignAnchoredThreads || threadOriginTop == null) return margins;
410	    let cursor = 0;
411	    for (const root of orderedVisibleRoots) {
412	      const position = anchorPositionById.get(root.id);
413	      const target = position ? Math.max(0, position.top - threadOriginTop) : cursor;
414	      const marginTop = Math.max(0, target - cursor);
415	      margins.set(root.id, Math.round(marginTop));
416	      cursor += marginTop + (threadHeights[root.id] ?? 80) + 8;
417	    }
418	    return margins;
419	  }, [alignAnchoredThreads, anchorPositionById, orderedVisibleRoots, threadHeights, threadOriginTop]);
420	
421	  function renderComment(c: Comment, isReply = false, replyCount = 0) {
422	    const isAgent = c.authorKind === 'claude' || c.authorKind === 'codex';
423	    const collapsed = collapsedIds.has(c.id);
424	    const displayBody = visibleBody(c);
425	    const hoverable = !isReply && !!c.anchoredQuote && !!anchorCtx;
426	    const isHovered = hoverable && anchorCtx?.hoveredId === c.id;
427	    const agentLabel = agentStatusLabel(c);
428	    const agentActive = Boolean(c.agentRunStatus && activeAgentStatuses.has(c.agentRunStatus));
429	    const scrolledPast =
430	      alignAnchoredThreads && !isReply && scrolledPastIds.has(c.id) && !isHovered;
431	    const wrap = `group p-3 transition-all duration-150 ${c.resolvedAt ? 'opacity-60' : ''} ${isAgent ? 'bg-[--color-muted-bg]' : ''} ${isReply ? 'border-l-2 border-[--color-border] ml-4' : ''} ${isHovered ? 'bg-[color-mix(in_srgb,var(--color-accent)_12%,transparent)]' : ''} ${scrolledPast ? 'max-h-9 overflow-hidden opacity-50 hover:opacity-100 hover:max-h-none' : ''}`;
432	    return (
433	      <article
434	        key={c.id}
435	        className={wrap}
436	        onMouseEnter={hoverable ? () => anchorCtx?.setHoveredId(c.id) : undefined}
437	        onMouseLeave={hoverable ? () => anchorCtx?.setHoveredId(null) : undefined}
438	      >
439	        <header c…

tool=Read

Read

1	'use client';
2	
3	import {
4	  createContext,
5	  useCallback,
6	  useContext,
7	  useMemo,
8	  useState,
9	  type ReactNode,
10	} from 'react';
11	
12	export interface AnchorRecord {
13	  id: string;
14	  quote: string;
15	}
16	
17	export interface AnchorPosition {
18	  id: string;
19	  top: number;
20	  height: number;
21	  found: boolean;
22	}
23	
24	export interface PendingAnchor {
25	  quote: string;
26	}
27	
28	interface AnchoredCommentsValue {
29	  anchors: AnchorRecord[];
30	  setAnchors: (anchors: AnchorRecord[]) => void;
31	  anchorPositions: AnchorPosition[];
32	  setAnchorPositions: (positions: AnchorPosition[]) => void;
33	  hoveredId: string | null;
34	  setHoveredId: (id: string | null) => void;
35	  pendingAnchor: PendingAnchor | null;
36	  setPendingAnchor: (anchor: PendingAnchor | null) => void;
37	  scrollToCommentId: string | null;
38	  requestScrollTo: (id: string) => void;
39	  clearScrollRequest: () => void;
40	}
41	
42	const Ctx = createContext<AnchoredCommentsValue | null>(null);
43	
44	export function AnchoredCommentsProvider({
45	  children,
46	  initialAnchors,
47	}: {
48	  children: ReactNode;
49	  initialAnchors?: AnchorRecord[];
50	}) {
51	  const [anchors, setAnchors] = useState<AnchorRecord[]>(initialAnchors ?? []);
52	  const [anchorPositions, setAnchorPositionRows] = useState<AnchorPosition[]>([]);
53	  const [hoveredId, setHoveredId] = useState<string | null>(null);
54	  const [pendingAnchor, setPendingAnchor] = useState<PendingAnchor | null>(null);
55	  const [scrollToCommentId, setScrollToCommentId] = useState<string | null>(null);
56	
57	  const requestScrollTo = useCallback((id: string) => setScrollToCommentId(id), []);
58	  const clearScrollRequest = useCallback(() => setScrollToCommentId(null), []);
59	  const setAnchorPositions = useCallback((positions: AnchorPosition[]) => {
60	    setAnchorPositionRows((prev) => (sameAnchorPositions(prev, positions) ? prev : positions));
61	  }, []);
62	
63	  const value = useMemo<AnchoredCommentsValue>(
64	    () => ({
65	      anchors,
66	      setAnchors,
67	      anchorPositions,
68	      setAnchorPositions,
69	      hoveredId,
70	      setHoveredId,
71	      pendingAnchor,
72	      setPendingAnchor,
73	      scrollToCommentId,
74	      requestScrollTo,
75	      clearScrollRequest,
76	    }),
77	    [anchors, anchorPositions, setAnchorPositions, hoveredId, pendingAnchor, scrollToCommentId, requestScrollTo, clearScrollRequest],
78	  );
79	
80	  return <Ctx.Provider value={value}>{children}</Ctx.Provider>;
81	}
82	
83	export function useAnchoredComments() {
84	  return useContext(Ctx);
85	}
86	
87	function sameAnchorPositions(a: AnchorPosition[], b: AnchorPosition[]) {
88	  if (a.length !== b.length) return false;
89	  for (let i = 0; i < a.length; i++) {
90	    const left = a[i]!;
91	    const right = b[i]!;
92	    if (
93	      left.id !== right.id ||
94	      left.top !== right.top ||
95	      left.height !== right.height ||
96	      left.found !== right.found
97	    ) {
98	      return false;
99	    }
100	  }
101	  return true;
102	}
103	

tool=Read

Read

1	'use client';
2	
3	import { memo, useCallback, useEffect, useRef, useState, type RefObject } from 'react';
4	import { Markdown } from './Markdown';
5	import {
6	  useAnchoredComments,
7	  type AnchorRecord,
8	} from './AnchoredCommentsContext';
9	
10	/**
11	 * Render a narrative body. If the body looks like raw HTML (starts with
12	 * an HTML tag after whitespace), inject it via dangerouslySetInnerHTML so
13	 * Claude-authored HTML artifacts render with their own inline styles +
14	 * SVG. Otherwise fall through to Markdown rendering.
15	 *
16	 * When wrapped in an AnchoredCommentsProvider, this component also:
17	 *   - wraps each anchored quote in a <mark data-comment-id>
18	 *   - shows a floating "Comment" button on text selection
19	 *   - syncs hover state with the comments sidebar
20	 *
21	 * Trust model: project_narratives writes require an authenticated session.
22	 */
23	export function NarrativeBody({ body }: { body: string }) {
24	  const trimmed = body.trimStart();
25	  const looksHtml =
26	    trimmed.startsWith('<!DOCTYPE') ||
27	    trimmed.startsWith('<html') ||
28	    trimmed.startsWith('<div') ||
29	    trimmed.startsWith('<section') ||
30	    trimmed.startsWith('<article') ||
31	    trimmed.startsWith('<main') ||
32	    trimmed.startsWith('<style');
33	
34	  return looksHtml ? <HtmlNarrative body={body} /> : <MarkdownNarrative body={body} />;
35	}
36	
37	function HtmlNarrative({ body }: { body: string }) {
38	  // The inner HTML lives in a memo'd child so popover/anchor state changes in
39	  // useAnchorBehaviors don't cause React to touch dangerouslySetInnerHTML —
40	  // React 19 was rebuilding the children on every parent render, which wiped
41	  // out the user's text selection.
42	  const ref = useRef<HTMLDivElement>(null);
43	  useAnchorBehaviors(ref);
44	  return (
45	    <div ref={ref} className="narrative-html relative">
46	      <HtmlInner body={body} />
47	    </div>
48	  );
49	}
50	
51	const HtmlInner = memo(function HtmlInner({ body }: { body: string }) {
52	  return (
53	    <div
54	      // biome-ignore lint/security/noDangerouslySetInnerHtml: author is trusted (auth-gated write)
55	      dangerouslySetInnerHTML={{ __html: body }}
56	    />
57	  );
58	});
59	
60	function MarkdownNarrative({ body }: { body: string }) {
61	  const ref = useRef<HTMLDivElement>(null);
62	  useAnchorBehaviors(ref);
63	  return (
64	    <div ref={ref} className="relative">
65	      <MarkdownInner body={body} />
66	    </div>
67	  );
68	}
69	
70	const MarkdownInner = memo(function MarkdownInner({ body }: { body: string }) {
71	  return <Markdown>{body}</Markdown>;
72	});
73	
74	/**
75	 * Manage anchor wrapping, hover sync, scroll-to-mark, and the floating
76	 * "Comment" selection popover. Returns nothing when no anchor context is
77	 * present, leaving the narrative untouched.
78	 */
79	export function useAnchorBehaviors(ref: RefObject<HTMLDivElement | null>) {
80	  const ctx = useAnchoredComments();
81	  const [popover, setPopover] = useState<{
82	    left: number;
83	    top: number;
84	    quote: string;
85	  } | null>(null);
86	
87	  const anchors = ctx?.anchors;
88	  const setAnchorPositions = ctx?.setAnchorPositions;
89	  const hoveredId = ctx?.hoveredId ?? null;
90	  const setHoveredId = ctx?.setHoveredId;
91	  const scrollToCommentId = ctx?.scrollToCommentId ?? null;
92	  const clearScrollRequest = ctx?.clearScrollRequest;
93	  const setPendingAnchor = ctx?.setPendingAnchor;
94	  const pendingAnchor = ctx?.pendingAnchor ?? null;
95	
96	  const measureAnchors = useCallback(() => {
97	    if (!setAnchorPositions) return;
98	    if (!ref.current || !anchors || anchors.length === 0) {
99	      setAnchorPositions([]);
100	      return;
101	    }
102	    setAnchorPositions(measureAnchorPositions(ref.current, anchors));
103	  }, [anchors, ref, setAnchorPositions]);
104	
105	  // When pendingAnchor is cleared (submit success or × clicked) drop the
106	  // transient highlight. While pendingAnchor is set, the mark…

Found the cause. The Comments component polls `/api/comments` every 4 seconds and unconditionally calls `setAnchors(...)` with a brand-new array reference, even when the content is identical. That cascades into:
1. `anchors` state changes reference → 2. `applyAnchors` unwraps and re-wraps every `<mark>` in the narrative body → 3. `measureAnchors` reports new positions → 4. `threadMargins` recomputes → 5. each thread's `margin-top` animates via the `transition-[margin-top] duration-150` class. That's the visible jump on a 4s cadence.

`setAnchorPositions` already has a content-equality guard; `setAnchors` does not. Adding the same guard breaks the chain.

tool=Edit

edited /home/thomasjiralerspong/sagan/apps/web/src/components/AnchoredCommentsContext.tsx

tool=Edit

Edit

The file /home/thomasjiralerspong/sagan/apps/web/src/components/AnchoredCommentsContext.tsx has been updated successfully. (file state is current in your context — no need to Read it back)

tool=Edit

edited /home/thomasjiralerspong/sagan/apps/web/src/components/AnchoredCommentsContext.tsx

tool=Edit

Edit

The file /home/thomasjiralerspong/sagan/apps/web/src/components/AnchoredCommentsContext.tsx has been updated successfully. (file state is current in your context — no need to Read it back)

tool=Bash

Bash

> @sagan/web@0.0.0 typecheck /home/thomasjiralerspong/sagan/apps/web
> tsc --noEmit

tool=Bash

Bash

 M apps/web/src/components/AnchoredCommentsContext.tsx
?? .env.neon-backup-20260513
---
 apps/web/src/components/AnchoredCommentsContext.tsx | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

tool=Bash

Bash

[main 5a673bd] fix(comments): stop sidebar threads from jumping every 4s
 1 file changed, 16 insertions(+), 2 deletions(-)

tool=Bash

Bash

To https://github.com/superkaiba/sagan.git
   fd702c1..5a673bd  main -> main

Done with both halves.

**1. Phrasing edit.** The anchored span lived in the Murray paragraph (line 58 of the body). Rewrote it through `PATCH /api/project-narratives/f8cf6090…`:

- Before: *"…and that concentration alone is enough to route the word's queries to code"*
- After: *"…and that concentration alone is enough to make the model treat any prompt that uses* elucidate *as a coding request, even when the user wasn't asking about code"*

Verified the new text is live in `project_narratives.body_md`.

**2. Jumping threads — investigated and fixed.** Not a hallucination on your end. Mechanism:

- `Comments.tsx` polls `/api/comments` every 4 s and unconditionally runs `setItems(data.comments)` and `anchorCtx.setAnchors(next)` with brand-new array references.
- `setAnchorPositions` already had a content-equality guard in `AnchoredCommentsContext.tsx`, but `setAnchors` did not — so every poll changed the `anchors` state reference.
- That re-fired `NarrativeBody`'s `applyAnchors` effect, which calls `unwrapAllMarks` then re-wraps every `<mark data-comment-id>` in the body. The rAF-scheduled `measureAnchors` then handed Comments a (sometimes subpixel-rounded) new `anchorPositions`, which fed `threadMargins`, which combined with the `transition-[margin-top] duration-150 ease-out` class on each thread to animate the whole sidebar.

Fix: add a `sameAnchors` equality guard at the context boundary so `setAnchors` is a no-op when the list content is unchanged. Mirrors what `setAnchorPositions` already does. `pnpm typecheck` clean.

Commit: [`5a673bd`](https://github.com/superkaiba/sagan/commit/5a673bd) — `fix(comments): stop sidebar threads from jumping every 4s`. Pushed to `main`; Vercel will build and deploy to `sagan.superkaiba.com` momentarily. Hard-refresh once the deployment goes green and the rail should sit still between polls.

<<<DONE>>>

success

Done with both halves.

**1. Phrasing edit.** The anchored span lived in the Murray paragraph (line 58 of the body). Rewrote it through `PATCH /api/project-narratives/f8cf6090…`:

- Before: *"…and that concentration alone is enough to route the word's queries to code"*
- After: *"…and that concentration alone is enough to make the model treat any prompt that uses* elucidate *as a coding request, even when the user wasn't asking about code"*

Verified the new text is live in `project_narratives.body_md`.

**2. Jumping threads — investigated and fixed.** Not a hallucination on your end. Mechanism:

- `Comments.tsx` polls `/api/comments` every 4 s and unconditionally runs `setItems(data.comments)` and `anchorCtx.setAnchors(next)` with brand-new array references.
- `setAnchorPositions` already had a content-equality guard in `AnchoredCommentsContext.tsx`, but `setAnchors` did not — so every poll changed the `anchors` state reference.
- That re-fired `NarrativeBody`'s `applyAnchors` effect,…