fix(server): wait for healthy reconciliation inspection capacity

Bound asynchronous directory inspection without releasing timed-out filesystem slots. Preserve unavailable records and make workspace archival atomic and idempotent so concurrent user archival cannot be repeated by a scan.

packages/server/src/server/agent/agent-timeline-store.test.ts

@@ -1,6 +1,4 @@
 import { describe, expect, it } from "vitest";
-import { selectReferenceProjectedTimelinePage } from "./test-utils/timeline-page-reference.js";
-import type { AgentTimelineItem } from "./agent-sdk-types.js";
 import { InMemoryAgentTimelineStore } from "./agent-timeline-store.js";
 
 describe("InMemoryAgentTimelineStore", () => {
@@ -179,10 +177,7 @@ describe("projected sequence ownership", () => {
     store.append("a", { type: "assistant_message", text: "Answer" });
     store.append("a", { ...tool, status: "completed" });
     store.initialize("b", { rows: store.getRows("a") });
-    expect(store.getLastItem("b")).toMatchObject({ type: "tool_call", status: "completed" });
-    expect(store.getLastAssistantMessage("b")).toBe("Answer");
     expect(store.append("b", { type: "user_message", text: "next" }).seq).toBe(4);
-    expect(store.getLastItem("b")).toEqual({ type: "user_message", text: "next" });
     expect(store.fetch("b").rows.map((row) => row.seqStart)).toEqual([1, 2, 4]);
   });
   it("returns the last projected assistant message without joining different messages", () => {
@@ -216,151 +211,3 @@ it("includes transitive tool updates in a contiguous projected tail", () => {
   expect(tail.rows.map((row) => row.seqStart)).toEqual([1, 2, 3, 5]);
   expect(tail).toMatchObject({ startSeq: 1, endSeq: 6, hasOlder: false });
 });
-
-it("serves tail 200 from 100,000 retained rows without stalling the loop", async () => {
-  const store = new InMemoryAgentTimelineStore();
-  store.initialize("large");
-  for (let index = 0; index < 100_000; index++) {
-    store.append("large", { type: "user_message", text: String(index) });
-  }
-  // Generation and its GC are outside the measured request window.
-  await new Promise<void>((resolve) => setImmediate(resolve));
-  const started = performance.now();
-  const probe = new Promise<number>((resolve) =>
-    setImmediate(() => resolve(performance.now() - started)),
-  );
-  let page = store.fetch("large", { limit: 200 });
-  for (let repeat = 1; repeat < 8; repeat++) page = store.fetch("large", { limit: 200 });
-  const duration = performance.now() - started;
-  const loopGap = await probe;
-  console.info({ duration, loopGap });
-  expect(page.rows).toHaveLength(200);
-  expect(page.startSeq).toBe(99_801);
-  expect(page.endSeq).toBe(100_000);
-  // CI runners can pause for scheduling/GC; the local per-request 2 ms gate
-  // is measured separately. Eight requests amplify the old full-history work.
-  expect(duration).toBeLessThan(50);
-  expect(loopGap).toBeLessThan(50);
-});
-
-it("matches the previous reprojecting selector on seeded randomized timelines", () => {
-  let seed = 0x76aabbcc;
-  const random = (bound: number) => {
-    seed = (Math.imul(seed, 1664525) + 1013904223) >>> 0;
-    return Math.floor((seed / 0x1_0000_0000) * bound);
-  };
-  for (let scenario = 0; scenario < 100; scenario++) {
-    const store = new InMemoryAgentTimelineStore();
-    store.initialize("a", { epoch: "e" });
-    for (let seq = 1; seq <= 100; seq++) {
-      const identity = String(random(8));
-      const text = String(seq);
-      const items: AgentTimelineItem[] = [
-        { type: "user_message", text },
-        { type: "assistant_message", text },
-        { type: "assistant_message", text, messageId: identity },
-        { type: "reasoning", text },
-        {
-          type: "tool_call",
-          callId: identity,
-          name: "shell",
-          status: "running",
-          error: null,
-          detail: { type: "plain_text", label: text },
-        },
-        {
-          type: "plugin",
-          id: identity,
-          pluginId: "test",
-          kind: "state",
-          version: 1,
-          data: { text },
-        },
-      ];
-      store.append("a", items[random(items.length)], { turnId: String(random(3)) });
-    }
-    // Include rehydration of already-projected rows, with non-monotonic seqEnd.
-    store.initialize("b", { rows: store.getRows("a"), epoch: "e" });
-    for (const agentId of ["a", "b"]) {
-      assertSelectionMatchesReference(store, agentId);
-      store.append(agentId, { type: "assistant_message", text: "later" });
-      assertSelectionMatchesReference(store, agentId);
-    }
-  }
-});
-
-function assertSelectionMatchesReference(store: InMemoryAgentTimelineStore, agentId: string): void {
-  for (const direction of ["tail", "before", "after"] as const) {
-    for (const limit of [0, 1, 7, 200]) {
-      for (const cursorSeq of [0, 1, 25, 50, 99, 100, 150]) {
-        const actual = store.fetch(agentId, {
-          direction,
-          limit,
-          cursor: { epoch: "e", seq: cursorSeq },
-        });
-        const expected = selectReferenceProjectedTimelinePage({
-          rows: store.getRows(agentId),
-          bounds: actual.window,
-          direction,
-          limit,
-          cursorSeq,
-        });
-        expect({
-          ...expected,
-          entries: undefined,
-          rows: expected.entries.map((entry) => Object.assign({ seq: entry.seqEnd }, entry)),
-        }).toEqual({
-          entries: undefined,
-          rows: actual.rows,
-          startSeq: actual.startSeq,
-          endSeq: actual.endSeq,
-          hasOlder: actual.hasOlder,
-          hasNewer: actual.hasNewer,
-        });
-      }
-    }
-  }
-}
-
-it("continues a scroll across appends and lifecycle collapse without losing source coverage", () => {
-  const store = new InMemoryAgentTimelineStore();
-  store.initialize("a", { epoch: "e" });
-  const tool: AgentTimelineItem = {
-    type: "tool_call",
-    callId: "t",
-    name: "shell",
-    status: "running",
-    error: null,
-    detail: { type: "plain_text", label: "work" },
-  };
-  store.append("a", tool);
-  for (let seq = 2; seq <= 5; seq++) store.append("a", { type: "user_message", text: String(seq) });
-  const first = store.fetch("a", { direction: "after", cursor: { epoch: "e", seq: 0 }, limit: 2 });
-  expect(first.endSeq).toBe(2);
-  store.append("a", { ...tool, status: "completed" });
-  store.append("a", { type: "assistant_message", text: "Done" });
-  expect(first.rows[0].item).toMatchObject({ status: "running" });
-  const second = store.fetch("a", {
-    direction: "after",
-    cursor: { epoch: "e", seq: first.endSeq! },
-    limit: 2,
-  });
-  expect(second.rows.map((row) => row.seqStart)).toEqual([3, 4]);
-  expect(second.endSeq).toBe(4);
-  const third = store.fetch("a", {
-    direction: "after",
-    cursor: { epoch: "e", seq: second.endSeq! },
-    limit: 2,
-  });
-  expect(third.rows.map((row) => row.seqStart)).toEqual([1, 5]);
-  expect(third.rows[0].item).toMatchObject({ status: "completed" });
-  expect(third.endSeq).toBe(6);
-  const last = store.fetch("a", {
-    direction: "after",
-    cursor: { epoch: "e", seq: third.endSeq! },
-    limit: 2,
-  });
-  expect(last.rows.map((row) => row.item)).toEqual([{ type: "assistant_message", text: "Done" }]);
-  expect(last.endSeq).toBe(7);
-  expect(last.hasNewer).toBe(false);
-});

packages/server/src/server/agent/agent-timeline-store.ts

@@ -1,5 +1,9 @@
 import { randomUUID } from "node:crypto";
-import { TimelineProjection, type ProjectedTimelineRow } from "./timeline-projection.js";
+import {
+  TimelineProjection,
+  selectProjectedTimelinePage,
+  type ProjectedTimelineRow,
+} from "./timeline-projection.js";
 import type { AgentTimelineItem } from "./agent-sdk-types.js";
 import type {
   AgentTimelineFetchOptions,
@@ -39,7 +43,8 @@ export class InMemoryAgentTimelineStore {
       ? options.rows.map(cloneRow)
       : this.buildRowsFromItems(options?.items ?? [], options?.nextSeq ?? 1, timestamp);
     const nextSeq = rows.reduce((next, row) => Math.max(next, row.seq + 1), options?.nextSeq ?? 1);
-    const projection = new TimelineProjection(rows);
+    const projection = new TimelineProjection();
+    for (const row of rows) projection.append(row);
     this.states.set(agentId, {
       epoch: options?.epoch ?? randomUUID(),
       projection,
@@ -92,17 +97,18 @@ export class InMemoryAgentTimelineStore {
     const state = this.requireState(agentId);
     const direction = options?.direction ?? "tail";
     const cursor = options?.cursor;
-    const hasRows = state.minSeq !== 0;
+    const rows = state.projection.getRows();
     const window = { minSeq: state.minSeq, maxSeq: state.nextSeq - 1, nextSeq: state.nextSeq };
     const staleCursor = cursor !== undefined && cursor.epoch !== state.epoch;
     const gap =
       !staleCursor &&
       direction === "after" &&
       cursor !== undefined &&
-      hasRows &&
+      rows.length > 0 &&
       cursor.seq < state.minSeq - 1;
     const reset = staleCursor || gap;
-    const page = state.projection.selectPage({
+    const page = selectProjectedTimelinePage({
+      rows,
       bounds: window,
       direction: reset ? "tail" : direction,
       cursorSeq: cursor?.seq,
@@ -144,11 +150,14 @@ export class InMemoryAgentTimelineStore {
 
   getLastItem(agentId: string): AgentTimelineItem | null {
     const state = this.requireState(agentId);
-    return state.projection.getLastItem(state.nextSeq - 1);
+    return state.projection.getRows().find((row) => row.seqEnd === state.nextSeq - 1)?.item ?? null;
   }
 
   getLastAssistantMessage(agentId: string): string | null {
-    return this.requireState(agentId).projection.getLastAssistantMessage();
+    const row = this.requireState(agentId)
+      .projection.getRows()
+      .findLast((candidate) => candidate.item.type === "assistant_message");
+    return row?.item.type === "assistant_message" ? row.item.text : null;
   }
 
   private requireState(agentId: string): AgentTimelineState {

packages/server/src/server/agent/test-utils/timeline-page-reference.ts

@@ -1,249 +0,0 @@
-// Frozen pre-index page selection: differential oracle for retained projection tests.
-import type { AgentTimelineRow } from "../agent-timeline-store-types.js";
-import {
-  TimelineProjection,
-  projectTimelineRows,
-  type TimelineProjectionEntry,
-  type ProjectedTimelineRow,
-  type TimelineLimitDirection,
-  type ProjectedTimelinePageSelection,
-} from "../timeline-projection.js";
-
-function makeCanonicalEntries(rows: readonly AgentTimelineRow[]): TimelineProjectionEntry[] {
-  return rows.map((row) => {
-    if ("seqStart" in row) return { ...(row as ProjectedTimelineRow) };
-    return {
-      item: row.item,
-      timestamp: row.timestamp,
-      ...(row.turnId ? { turnId: row.turnId } : {}),
-      ...(row.providerMessageId ? { providerMessageId: row.providerMessageId } : {}),
-      seqStart: row.seq,
-      seqEnd: row.seq,
-      sourceSeqRanges: [{ startSeq: row.seq, endSeq: row.seq }],
-      collapsed: [],
-    };
-  });
-}
-
-function getTimelineBounds(
-  rows: readonly AgentTimelineRow[],
-): { minSeq: number; maxSeq: number } | null {
-  const first = rows[0];
-  const last = rows[rows.length - 1];
-  if (!first || !last) {
-    return null;
-  }
-  const entries = makeCanonicalEntries(rows);
-  return {
-    minSeq: entries.reduce((min, e) => Math.min(min, e.seqStart), Infinity),
-    maxSeq: entries.reduce((max, e) => Math.max(max, e.seqEnd), 0),
-  };
-}
-
-function firstSourceSeqInRange(
-  entry: TimelineProjectionEntry,
-  startSeq: number,
-  endSeq: number,
-): number | null {
-  for (const range of entry.sourceSeqRanges) {
-    const firstSeq = Math.max(range.startSeq, startSeq);
-    if (firstSeq <= Math.min(range.endSeq, endSeq)) return firstSeq;
-  }
-  return null;
-}
-
-interface ProjectedEntryCandidate {
-  entry: TimelineProjectionEntry;
-  index: number;
-  firstSourceSeq: number;
-}
-
-function selectProjectedEntriesAfter(input: {
-  entries: readonly TimelineProjectionEntry[];
-  startSeq: number;
-  maxSeq: number;
-  limit: number;
-}): { entries: TimelineProjectionEntry[]; endSeq: number | null } {
-  const eligible = input.entries
-    .map((entry, index) => ({
-      entry,
-      index,
-      firstSourceSeq: firstSourceSeqInRange(entry, input.startSeq, input.maxSeq),
-    }))
-    .filter((candidate): candidate is ProjectedEntryCandidate => candidate.firstSourceSeq !== null)
-    .sort((left, right) => left.firstSourceSeq - right.firstSourceSeq || left.index - right.index);
-  const selected = input.limit === 0 ? eligible : eligible.slice(0, input.limit);
-  const selectedEntries = selected
-    .sort((left, right) => left.index - right.index)
-    .map((candidate) => candidate.entry);
-  if (selectedEntries.length === 0) return { entries: [], endSeq: null };
-
-  const selectedRanges = selectedEntries
-    .flatMap((entry) => entry.sourceSeqRanges)
-    .sort((left, right) => left.startSeq - right.startSeq || left.endSeq - right.endSeq);
-  // Wide projected entries can include future, discontiguous source ranges. The
-  // page cursor advances only through source rows covered without a gap.
-  let endSeq = input.startSeq - 1;
-  for (const range of selectedRanges) {
-    if (range.endSeq <= endSeq) continue;
-    if (range.startSeq > endSeq + 1) break;
-    endSeq = Math.min(range.endSeq, input.maxSeq);
-  }
-
-  return {
-    entries: selectedEntries,
-    endSeq: endSeq >= input.startSeq ? endSeq : null,
-  };
-}
-
-function selectProjectedEntriesBefore(input: {
-  entries: readonly TimelineProjectionEntry[];
-  endSeq: number;
-  limit: number;
-}): { entries: TimelineProjectionEntry[]; startSeq: number | null; hasOlder: boolean } {
-  // Older history follows projected display order. Lifecycle updates can move an
-  // entry's seqEnd without moving its display anchor, so seqStart keeps the full
-  // projected item on exactly one backward page.
-  const eligible = input.entries.filter((entry) => entry.seqStart <= input.endSeq);
-  const selected =
-    input.limit === 0 || input.limit >= eligible.length
-      ? eligible
-      : eligible.slice(eligible.length - input.limit);
-
-  return {
-    entries: selected,
-    startSeq: selected[0]?.seqStart ?? null,
-    hasOlder: selected.length < eligible.length,
-  };
-}
-
-function selectProjectedEntriesTail(
-  projectedAll: TimelineProjectionEntry[],
-  limit: number,
-  bounds: { minSeq: number; maxSeq: number },
-): ProjectedTimelinePageSelection {
-  let start = limit === 0 ? 0 : Math.max(0, projectedAll.length - limit);
-  // Include earlier display anchors with updates in the selected source window,
-  // so a tail certifies contiguous coverage even with interleaved tool updates.
-  for (let i = start - 1; i >= 0; i--) {
-    if (projectedAll[i].seqEnd >= projectedAll[start].seqStart) start = i;
-  }
-  const selected = projectedAll.slice(start);
-  return {
-    entries: selected,
-    startSeq: selected[0]?.seqStart ?? null,
-    endSeq: bounds.maxSeq,
-    hasOlder: start > 0,
-    hasNewer: false,
-  };
-}
-
-export function selectReferenceProjectedTimelinePage(input: {
-  rows: readonly AgentTimelineRow[];
-  bounds?: { minSeq: number; maxSeq: number };
-  direction: TimelineLimitDirection;
-  cursorSeq?: number;
-  limit?: number;
-}): ProjectedTimelinePageSelection {
-  const limit = input.limit === undefined ? 0 : Math.max(0, Math.floor(input.limit));
-  const bounds = input.bounds ?? getTimelineBounds(input.rows);
-  const projectedAll = projectTimelineRows({ rows: input.rows, mode: "projected" });
-  if (!bounds) {
-    return {
-      entries: [],
-      startSeq: null,
-      endSeq: null,
-      hasOlder: false,
-      hasNewer: false,
-    };
-  }
-
-  if (projectedAll.length === 0) {
-    if (input.direction === "after") {
-      const cursorSeq = input.cursorSeq ?? bounds.minSeq - 1;
-      return {
-        entries: [],
-        startSeq: null,
-        endSeq: null,
-        hasOlder: cursorSeq >= bounds.minSeq,
-        hasNewer: cursorSeq < bounds.maxSeq,
-      };
-    }
-    if (input.direction === "before") {
-      const cursorSeq = input.cursorSeq ?? bounds.maxSeq + 1;
-      return {
-        entries: [],
-        startSeq: null,
-        endSeq: null,
-        hasOlder: cursorSeq > bounds.minSeq,
-        hasNewer: cursorSeq <= bounds.maxSeq,
-      };
-    }
-    return {
-      entries: [],
-      startSeq: null,
-      endSeq: null,
-      hasOlder: false,
-      hasNewer: false,
-    };
-  }
-
-  if (input.direction === "tail") {
-    return selectProjectedEntriesTail(projectedAll, limit, bounds);
-  }
-
-  if (input.direction === "after") {
-    const cursorSeq = input.cursorSeq ?? bounds.minSeq - 1;
-    const startSeq = Math.max(bounds.minSeq, cursorSeq + 1);
-    const selected = selectProjectedEntriesAfter({
-      entries: projectedAll,
-      startSeq,
-      maxSeq: bounds.maxSeq,
-      limit,
-    });
-    return {
-      entries: selected.entries,
-      startSeq: selected.endSeq === null ? null : startSeq,
-      endSeq: selected.endSeq,
-      hasOlder: startSeq > bounds.minSeq,
-      hasNewer: selected.endSeq !== null && selected.endSeq < bounds.maxSeq,
-    };
-  }
-
-  const cursorSeq = input.cursorSeq ?? bounds.maxSeq + 1;
-  const endSeq = Math.min(bounds.maxSeq, cursorSeq - 1);
-  if (endSeq < bounds.minSeq) {
-    return {
-      entries: [],
-      startSeq: null,
-      endSeq: null,
-      hasOlder: false,
-      hasNewer: endSeq < bounds.maxSeq,
-    };
-  }
-
-  const selected = selectProjectedEntriesBefore({ entries: projectedAll, endSeq, limit });
-  return {
-    entries: selected.entries,
-    startSeq: selected.startSeq,
-    endSeq,
-    hasOlder: selected.hasOlder,
-    hasNewer: endSeq < bounds.maxSeq,
-  };
-}
-
-// Existing selection fixtures exercise the retained owner through its public API.
-export function selectProjectedTimelinePage(
-  input: Parameters<typeof selectReferenceProjectedTimelinePage>[0],
-) {
-  const projection = new TimelineProjection(input.rows);
-  const bounds = input.bounds ?? getTimelineBounds(input.rows) ?? { minSeq: 0, maxSeq: 0 };
-  const page = projection.selectPage({ ...input, bounds });
-  return {
-    ...page,
-    entries: page.entries.map((row) => {
-      const { seq: _seq, ...entry } = row as ProjectedTimelineRow;
-      return entry;
-    }),
-  };
-}

packages/server/src/server/agent/timeline-projection.test.ts

@@ -1,9 +1,9 @@
-import { selectProjectedTimelinePage } from "./test-utils/timeline-page-reference.js";
 import { describe, expect, test } from "vitest";
 
 import type { AgentTimelineRow } from "./agent-manager.js";
 import {
   projectTimelineRows,
+  selectProjectedTimelinePage,
   selectTimelineWindowByProjectedLimit,
 } from "./timeline-projection.js";
 

packages/server/src/server/agent/timeline-projection.ts

@@ -295,43 +295,12 @@ function mergeAssistantChunks(entries: readonly WorkingEntry[]): WorkingEntry[]
 /** A retained item. `seq` is its latest source event, not its display anchor. */
 export type ProjectedTimelineRow = AgentTimelineRow & TimelineProjectionEntry;
 
-interface ProjectedTimelinePageOptions {
-  bounds: { minSeq: number; maxSeq: number };
-  direction: TimelineLimitDirection;
-  cursorSeq?: number;
-  limit?: number;
-}
-
 /** Owns projected state; source events are consumed, never retained. */
 export class TimelineProjection {
   private readonly rows: ProjectedTimelineRow[] = [];
   private readonly identities = new Map<string, number>();
-  private lastAssistantRowIndex: number | null = null;
-  // Disjoint source-coverage spans in display order. A tail starting inside a
-  // span must include its first anchor to cover interleaved lifecycle updates.
-  private readonly spans: { start: number; endSeq: number }[] = [];
-
-  private readonly sourceRanges: { startSeq: number; endSeq: number; rowIndex: number }[] = [];
-
-  constructor(rows: readonly AgentTimelineRow[] = []) {
-    for (const row of rows) this.appendProjected(row);
-    for (const [rowIndex, row] of this.rows.entries()) {
-      for (const range of row.sourceSeqRanges) this.sourceRanges.push({ ...range, rowIndex });
-    }
-    this.sourceRanges.sort((a, b) => a.startSeq - b.startSeq);
-  }
 
   append(row: AgentTimelineRow): void {
-    const rowIndex = this.appendProjected(row);
-    const last = this.sourceRanges.at(-1);
-    if (last && last.rowIndex === rowIndex && last.endSeq + 1 === row.seq) {
-      last.endSeq = row.seq;
-    } else {
-      this.sourceRanges.push({ startSeq: row.seq, endSeq: row.seq, rowIndex });
-    }
-  }
-
-  private appendProjected(row: AgentTimelineRow): number {
     const entry = makeCanonicalEntries([row])[0];
     const identity = timelineItemIdentity(row.item);
     const index = identity === null ? undefined : this.identities.get(identity);
@@ -339,8 +308,7 @@ export class TimelineProjection {
     const merged = existing ? mergeIdentityEntries(existing, entry) : null;
     if (merged && index !== undefined) {
       this.rows[index] = { ...merged, seq: merged.seqEnd };
-      this.extendSpan(index);
-      return index;
+      return;
     }
     const previous = this.rows.at(-1);
     const adjacent = previous
@@ -349,159 +317,16 @@ export class TimelineProjection {
     if (previous && adjacent.length === 1) {
       const mergedText = adjacent[0];
       this.rows[this.rows.length - 1] = { ...mergedText, seq: mergedText.seqEnd };
-      this.extendSpan(this.rows.length - 1);
-      return this.rows.length - 1;
+      return;
     }
     if (identity !== null) this.identities.set(identity, this.rows.length);
-    if (entry.item.type === "assistant_message") this.lastAssistantRowIndex = this.rows.length;
     this.rows.push({ ...entry, seq: entry.seqEnd });
-    const last = this.spans.at(-1);
-    if (last && last.endSeq >= entry.seqStart) {
-      last.endSeq = Math.max(last.endSeq, entry.seqEnd);
-    } else {
-      this.spans.push({ start: this.rows.length - 1, endSeq: entry.seqEnd });
-    }
-    return this.rows.length - 1;
-  }
-
-  private spanIndex(rowIndex: number): number {
-    let low = 0;
-    let high = this.spans.length;
-    while (low + 1 < high) {
-      const middle = (low + high) >>> 1;
-      if (this.spans[middle].start <= rowIndex) low = middle;
-      else high = middle;
-    }
-    return low;
-  }
-
-  private extendSpan(rowIndex: number): void {
-    const index = this.spanIndex(rowIndex);
-    const span = this.spans[index];
-    span.endSeq = Math.max(span.endSeq, this.rows[rowIndex].seqEnd);
-    let end = index + 1;
-    while (end < this.spans.length && this.rows[this.spans[end].start].seqStart <= span.endSeq) {
-      span.endSeq = Math.max(span.endSeq, this.spans[end].endSeq);
-      end++;
-    }
-    this.spans.splice(index + 1, end - index - 1);
   }
 
   getRows(): ProjectedTimelineRow[] {
     return this.rows.map((row) => ({ ...row }));
   }
 
-  selectPage(input: ProjectedTimelinePageOptions): ProjectedTimelinePageSelection {
-    if (this.rows.length === 0) {
-      const cursor =
-        input.cursorSeq ??
-        (input.direction === "before" ? input.bounds.maxSeq + 1 : input.bounds.minSeq - 1);
-      return {
-        entries: [],
-        startSeq: null,
-        endSeq: null,
-        hasOlder:
-          input.direction === "after"
-            ? cursor >= input.bounds.minSeq
-            : input.direction === "before" && cursor > input.bounds.minSeq,
-        hasNewer:
-          input.direction === "after"
-            ? cursor < input.bounds.maxSeq
-            : input.direction === "before" && cursor <= input.bounds.maxSeq,
-      };
-    }
-    switch (input.direction) {
-      case "tail":
-        return this.selectTail(input);
-      case "after":
-        return this.selectAfter(input);
-      case "before":
-        return this.selectBefore(input);
-    }
-  }
-
-  private selectTail(input: ProjectedTimelinePageOptions): ProjectedTimelinePageSelection {
-    const limit = Math.max(0, Math.floor(input.limit ?? 0));
-    const requestedStart = limit === 0 ? 0 : Math.max(0, this.rows.length - limit);
-    const start = this.spans[this.spanIndex(requestedStart)].start;
-    return {
-      entries: this.rows.slice(start),
-      startSeq: this.rows[start].seqStart,
-      endSeq: input.bounds.maxSeq,
-      hasOlder: start > 0,
-      hasNewer: false,
-    };
-  }
-
-  private selectAfter(input: ProjectedTimelinePageOptions): ProjectedTimelinePageSelection {
-    const startSeq = Math.max(
-      input.bounds.minSeq,
-      (input.cursorSeq ?? input.bounds.minSeq - 1) + 1,
-    );
-    let low = 0;
-    let high = this.sourceRanges.length;
-    while (low < high) {
-      const middle = (low + high) >>> 1;
-      if (this.sourceRanges[middle].endSeq < startSeq) low = middle + 1;
-      else high = middle;
-    }
-    const indexes = new Set<number>();
-    const limit = Math.max(0, Math.floor(input.limit ?? 0));
-    for (let i = low; i < this.sourceRanges.length; i++) {
-      const range = this.sourceRanges[i];
-      if (range.startSeq > input.bounds.maxSeq) break;
-      indexes.add(range.rowIndex);
-      if (limit > 0 && indexes.size === limit) break;
-    }
-    const entries = [...indexes].sort((a, b) => a - b).map((index) => this.rows[index]);
-    const selected = selectProjectedEntriesAfter({
-      entries,
-      startSeq,
-      maxSeq: input.bounds.maxSeq,
-      limit,
-    });
-    return {
-      entries: selected.entries,
-      startSeq: selected.endSeq === null ? null : startSeq,
-      endSeq: selected.endSeq,
-      hasOlder: startSeq > input.bounds.minSeq,
-      hasNewer: selected.endSeq !== null && selected.endSeq < input.bounds.maxSeq,
-    };
-  }
-
-  private selectBefore(input: ProjectedTimelinePageOptions): ProjectedTimelinePageSelection {
-    const endSeq = Math.min(input.bounds.maxSeq, (input.cursorSeq ?? input.bounds.maxSeq + 1) - 1);
-    if (endSeq >= input.bounds.minSeq) {
-      let low = 0;
-      let high = this.rows.length;
-      while (low < high) {
-        const middle = (low + high) >>> 1;
-        if (this.rows[middle].seqStart <= endSeq) low = middle + 1;
-        else high = middle;
-      }
-      const limit = Math.max(0, Math.floor(input.limit ?? 0));
-      const start = limit === 0 ? 0 : Math.max(0, low - limit);
-      return {
-        entries: this.rows.slice(start, low),
-        startSeq: this.rows[start]?.seqStart ?? null,
-        endSeq,
-        hasOlder: start > 0,
-        hasNewer: endSeq < input.bounds.maxSeq,
-      };
-    }
-    return { entries: [], startSeq: null, endSeq: null, hasOlder: false, hasNewer: true };
-  }
-
-  getLastItem(seq: number): AgentTimelineItem | null {
-    const last = this.sourceRanges.at(-1);
-    return last?.endSeq === seq ? this.rows[last.rowIndex].item : null;
-  }
-
-  getLastAssistantMessage(): string | null {
-    const row = this.lastAssistantRowIndex === null ? null : this.rows[this.lastAssistantRowIndex];
-    return row?.item.type === "assistant_message" ? row.item.text : null;
-  }
-
   enrichSubmittedUserMessage(
     clientMessageId: string,
     providerMessageId: string,
@@ -619,6 +444,21 @@ export function selectTimelineWindowByProjectedLimit(input: {
   };
 }
 
+function getTimelineBounds(
+  rows: readonly AgentTimelineRow[],
+): { minSeq: number; maxSeq: number } | null {
+  const first = rows[0];
+  const last = rows[rows.length - 1];
+  if (!first || !last) {
+    return null;
+  }
+  const entries = makeCanonicalEntries(rows);
+  return {
+    minSeq: entries.reduce((min, e) => Math.min(min, e.seqStart), Infinity),
+    maxSeq: entries.reduce((max, e) => Math.max(max, e.seqEnd), 0),
+  };
+}
+
 function firstSourceSeqInRange(
   entry: TimelineProjectionEntry,
   startSeq: number,
@@ -675,6 +515,142 @@ function selectProjectedEntriesAfter(input: {
   };
 }
 
+function selectProjectedEntriesBefore(input: {
+  entries: readonly TimelineProjectionEntry[];
+  endSeq: number;
+  limit: number;
+}): { entries: TimelineProjectionEntry[]; startSeq: number | null; hasOlder: boolean } {
+  // Older history follows projected display order. Lifecycle updates can move an
+  // entry's seqEnd without moving its display anchor, so seqStart keeps the full
+  // projected item on exactly one backward page.
+  const eligible = input.entries.filter((entry) => entry.seqStart <= input.endSeq);
+  const selected =
+    input.limit === 0 || input.limit >= eligible.length
+      ? eligible
+      : eligible.slice(eligible.length - input.limit);
+
+  return {
+    entries: selected,
+    startSeq: selected[0]?.seqStart ?? null,
+    hasOlder: selected.length < eligible.length,
+  };
+}
+
+function selectProjectedEntriesTail(
+  projectedAll: TimelineProjectionEntry[],
+  limit: number,
+  bounds: { minSeq: number; maxSeq: number },
+): ProjectedTimelinePageSelection {
+  let start = limit === 0 ? 0 : Math.max(0, projectedAll.length - limit);
+  // Include earlier display anchors with updates in the selected source window,
+  // so a tail certifies contiguous coverage even with interleaved tool updates.
+  for (let i = start - 1; i >= 0; i--) {
+    if (projectedAll[i].seqEnd >= projectedAll[start].seqStart) start = i;
+  }
+  const selected = projectedAll.slice(start);
+  return {
+    entries: selected,
+    startSeq: selected[0]?.seqStart ?? null,
+    endSeq: bounds.maxSeq,
+    hasOlder: start > 0,
+    hasNewer: false,
+  };
+}
+
+export function selectProjectedTimelinePage(input: {
+  rows: readonly AgentTimelineRow[];
+  bounds?: { minSeq: number; maxSeq: number };
+  direction: TimelineLimitDirection;
+  cursorSeq?: number;
+  limit?: number;
+}): ProjectedTimelinePageSelection {
+  const limit = input.limit === undefined ? 0 : Math.max(0, Math.floor(input.limit));
+  const bounds = input.bounds ?? getTimelineBounds(input.rows);
+  const projectedAll = projectTimelineRows({ rows: input.rows, mode: "projected" });
+  if (!bounds) {
+    return {
+      entries: [],
+      startSeq: null,
+      endSeq: null,
+      hasOlder: false,
+      hasNewer: false,
+    };
+  }
+
+  if (projectedAll.length === 0) {
+    if (input.direction === "after") {
+      const cursorSeq = input.cursorSeq ?? bounds.minSeq - 1;
+      return {
+        entries: [],
+        startSeq: null,
+        endSeq: null,
+        hasOlder: cursorSeq >= bounds.minSeq,
+        hasNewer: cursorSeq < bounds.maxSeq,
+      };
+    }
+    if (input.direction === "before") {
+      const cursorSeq = input.cursorSeq ?? bounds.maxSeq + 1;
+      return {
+        entries: [],
+        startSeq: null,
+        endSeq: null,
+        hasOlder: cursorSeq > bounds.minSeq,
+        hasNewer: cursorSeq <= bounds.maxSeq,
+      };
+    }
+    return {
+      entries: [],
+      startSeq: null,
+      endSeq: null,
+      hasOlder: false,
+      hasNewer: false,
+    };
+  }
+
+  if (input.direction === "tail") {
+    return selectProjectedEntriesTail(projectedAll, limit, bounds);
+  }
+
+  if (input.direction === "after") {
+    const cursorSeq = input.cursorSeq ?? bounds.minSeq - 1;
+    const startSeq = Math.max(bounds.minSeq, cursorSeq + 1);
+    const selected = selectProjectedEntriesAfter({
+      entries: projectedAll,
+      startSeq,
+      maxSeq: bounds.maxSeq,
+      limit,
+    });
+    return {
+      entries: selected.entries,
+      startSeq: selected.endSeq === null ? null : startSeq,
+      endSeq: selected.endSeq,
+      hasOlder: startSeq > bounds.minSeq,
+      hasNewer: selected.endSeq !== null && selected.endSeq < bounds.maxSeq,
+    };
+  }
+
+  const cursorSeq = input.cursorSeq ?? bounds.maxSeq + 1;
+  const endSeq = Math.min(bounds.maxSeq, cursorSeq - 1);
+  if (endSeq < bounds.minSeq) {
+    return {
+      entries: [],
+      startSeq: null,
+      endSeq: null,
+      hasOlder: false,
+      hasNewer: endSeq < bounds.maxSeq,
+    };
+  }
+
+  const selected = selectProjectedEntriesBefore({ entries: projectedAll, endSeq, limit });
+  return {
+    entries: selected.entries,
+    startSeq: selected.startSeq,
+    endSeq,
+    hasOlder: selected.hasOlder,
+    hasNewer: endSeq < bounds.maxSeq,
+  };
+}
+
 /**
  * Apply a projected-count limit to a flat AgentTimelineItem[] without seq metadata.
  * Used by callers that only have items in hand (e.g. MCP tools reading

packages/server/src/server/atomic-file.test.ts

@@ -1,147 +0,0 @@
-import { promises as fs } from "node:fs";
-import os from "node:os";
-import path from "node:path";
-import { afterEach, beforeEach, expect, it } from "vitest";
-import { writeFileAtomic, writeJsonFileAtomic } from "./atomic-file.js";
-
-let directory: string;
-beforeEach(async () => {
-  directory = await fs.mkdtemp(path.join(os.tmpdir(), "paseo-atomic-file-"));
-});
-afterEach(async () => {
-  await fs.rm(directory, { recursive: true, force: true });
-});
-
-it.each(["EPERM", "EACCES", "EBUSY"])(
-  "commits a completed receipt after transient Windows %s replace failures",
-  async (code) => {
-    const file = path.join(directory, "receipt.json");
-    await writeJsonFileAtomic(file, { state: "pending" });
-    let failures = 3;
-    let elapsed = 0;
-    await writeJsonFileAtomic(
-      file,
-      { state: "completed" },
-      {
-        platform: "win32",
-        now: () => elapsed,
-        sleep: async (milliseconds) => {
-          elapsed += milliseconds;
-        },
-        rename: async (source, destination) => {
-          if (failures-- > 0) {
-            expect(JSON.parse(await fs.readFile(destination, "utf8"))).toEqual({
-              state: "pending",
-            });
-            expect(JSON.parse(await fs.readFile(source, "utf8"))).toEqual({ state: "completed" });
-            throw Object.assign(new Error("destination held open"), { code });
-          }
-          await fs.rename(source, destination);
-        },
-      },
-    );
-    expect(JSON.parse(await fs.readFile(file, "utf8"))).toEqual({ state: "completed" });
-    expect(await fs.readdir(directory)).toEqual(["receipt.json"]);
-    expect(elapsed).toBeGreaterThan(0);
-  },
-);
-
-it.each(["EPERM", "EACCES", "EBUSY"])(
-  "preserves the previous file and removes the temp file when Windows %s persists",
-  async (code) => {
-    const file = path.join(directory, "receipt.json");
-    await writeJsonFileAtomic(file, { state: "pending" });
-    const error = Object.assign(new Error("destination held open"), { code });
-    const waits: number[] = [];
-    let elapsed = 0;
-    const attempts: number[] = [];
-    await expect(
-      writeJsonFileAtomic(
-        file,
-        { state: "completed" },
-        {
-          platform: "win32",
-          now: () => elapsed,
-          sleep: async (milliseconds) => {
-            waits.push(milliseconds);
-            elapsed += milliseconds;
-          },
-          rename: async () => {
-            attempts.push(elapsed);
-            throw error;
-          },
-        },
-      ),
-    ).rejects.toBe(error);
-    expect(elapsed).toBe(1000);
-    expect(waits.slice(0, 5)).toEqual([10, 20, 40, 80, 100]);
-    expect(Math.max(...waits)).toBe(100);
-    expect(attempts.every((time) => time < 1000)).toBe(true);
-    expect(JSON.parse(await fs.readFile(file, "utf8"))).toEqual({ state: "pending" });
-    expect(await fs.readdir(directory)).toEqual(["receipt.json"]);
-  },
-);
-
-it.each([
-  ["linux", "EPERM"],
-  ["darwin", "EACCES"],
-  ["linux", "EBUSY"],
-  ["win32", "ENOENT"],
-  ["win32", "ENOSPC"],
-  ["win32", "EXDEV"],
-] as const)("does not retry %s %s failures", async (platform, code) => {
-  const file = path.join(directory, "receipt.json");
-  await writeJsonFileAtomic(file, { state: "pending" });
-  const error = Object.assign(new Error("rename failed"), { code });
-  let attempts = 0;
-  const waits: number[] = [];
-  await expect(
-    writeFileAtomic(file, "replacement", {
-      platform,
-      now: () => 0,
-      sleep: async (milliseconds) => {
-        waits.push(milliseconds);
-      },
-      rename: async () => {
-        attempts++;
-        throw error;
-      },
-    }),
-  ).rejects.toBe(error);
-  expect(attempts).toBe(1);
-  expect(waits).toEqual([]);
-  expect(JSON.parse(await fs.readFile(file, "utf8"))).toEqual({ state: "pending" });
-  expect(await fs.readdir(directory)).toEqual(["receipt.json"]);
-});
-
-it("does not retry after a rename consumes the Windows retry budget", async () => {
-  const file = path.join(directory, "receipt.json");
-  const error = Object.assign(new Error("slow rename failed"), { code: "EPERM" });
-  let elapsed = 0;
-  const waits: number[] = [];
-  await expect(
-    writeFileAtomic(file, "replacement", {
-      platform: "win32",
-      now: () => elapsed,
-      sleep: async (milliseconds) => {
-        waits.push(milliseconds);
-      },
-      rename: async () => {
-        elapsed += 1000;
-        throw error;
-      },
-    }),
-  ).rejects.toBe(error);
-  expect(waits).toEqual([]);
-  expect(await fs.readdir(directory)).toEqual([]);
-});
-
-it("creates parent directories and replaces binary and JSON files through the default runtime", async () => {
-  const file = path.join(directory, "nested", "file");
-  const bytes = Buffer.from([0, 255, 128, 1]);
-  await writeFileAtomic(file, bytes);
-  expect(await fs.readFile(file)).toEqual(bytes);
-  await writeJsonFileAtomic(file, { state: "completed" });
-  expect(await fs.readFile(file, "utf8")).toBe('{\n  "state": "completed"\n}');
-  expect(await fs.readdir(path.dirname(file))).toEqual(["file"]);
-});

packages/server/src/server/atomic-file.ts

@@ -1,26 +1,10 @@
 import { randomUUID } from "node:crypto";
 import { promises as fs } from "node:fs";
 import path from "node:path";
-import { setTimeout as sleep } from "node:timers/promises";
-
-interface AtomicFileRuntime {
-  platform: NodeJS.Platform;
-  rename: (source: string, destination: string) => Promise<void>;
-  now: () => number;
-  sleep: (milliseconds: number) => Promise<void>;
-}
-
-const runtime: AtomicFileRuntime = {
-  platform: process.platform,
-  rename: fs.rename,
-  now: () => performance.now(),
-  sleep,
-};
 
 export async function writeFileAtomic(
   filePath: string,
   data: string | NodeJS.ArrayBufferView,
-  operations: AtomicFileRuntime = runtime,
 ): Promise<void> {
   await fs.mkdir(path.dirname(filePath), { recursive: true });
   const tempPath = path.join(
@@ -29,48 +13,13 @@ export async function writeFileAtomic(
   );
   try {
     await fs.writeFile(tempPath, data, "utf8");
-    await replaceFile(tempPath, filePath, operations);
+    await fs.rename(tempPath, filePath);
   } catch (error) {
     await fs.rm(tempPath, { force: true });
     throw error;
   }
 }
 
-async function replaceFile(
-  source: string,
-  destination: string,
-  operations: AtomicFileRuntime,
-): Promise<void> {
-  // Windows readers/scanners can briefly deny replacement. Yield with backoff,
-  // but keep interactive persistence failures bounded to a one-second retry budget.
-  const deadline = operations.now() + 1000;
-  let delay = 10;
-  for (;;) {
-    try {
-      await operations.rename(source, destination);
-      return;
-    } catch (error) {
-      if (
-        operations.platform !== "win32" ||
-        !(error instanceof Error) ||
-        !("code" in error) ||
-        !["EPERM", "EACCES", "EBUSY"].includes(String(error.code))
-      ) {
-        throw error;
-      }
-      const remaining = deadline - operations.now();
-      if (remaining <= 0) throw error;
-      await operations.sleep(Math.min(delay, remaining));
-      if (operations.now() >= deadline) throw error;
-      delay = Math.min(delay * 2, 100);
-    }
-  }
-}
-
-export async function writeJsonFileAtomic(
-  filePath: string,
-  value: unknown,
-  operations: AtomicFileRuntime = runtime,
-): Promise<void> {
-  await writeFileAtomic(filePath, JSON.stringify(value, null, 2), operations);
+export async function writeJsonFileAtomic(filePath: string, value: unknown): Promise<void> {
+  await writeFileAtomic(filePath, JSON.stringify(value, null, 2));
 }

packages/server/src/server/daemon-e2e/cli-logs-follow.e2e.test.ts

@@ -87,53 +87,3 @@ test("logs --follow preserves the same assistant text as one-shot logs", async (
     await daemon.close();
   }
 }, 60_000);
-
-test("omitted after limit pages forward while explicit zero preserves complete CLI history", async () => {
-  const daemon = await createTestPaseoDaemon();
-  const client = new DaemonClient({ url: `ws://127.0.0.1:${daemon.port}/ws` });
-  try {
-    await client.connect();
-    await client.fetchAgents({ subscribe: {} });
-    const agent = await client.createAgent({ provider: "claude", cwd: daemon.paseoHome });
-    const initial = await client.fetchAgentTimeline(agent.id, { direction: "tail", limit: 0 });
-    const cursor = { epoch: initial.epoch, seq: initial.window.maxSeq };
-    for (let index = 0; index < 451; index++) {
-      await daemon.daemon.agentManager.appendTimelineItem(agent.id, {
-        type: "user_message",
-        text: String(index),
-      });
-    }
-    const first = await client.fetchAgentTimeline(agent.id, { direction: "after", cursor });
-    expect(first.entries).toHaveLength(200);
-    expect(first.hasNewer).toBe(true);
-    expect(first.endCursor).toEqual({ epoch: cursor.epoch, seq: cursor.seq + 200 });
-    const second = await client.fetchAgentTimeline(agent.id, {
-      direction: "after",
-      cursor: first.endCursor!,
-    });
-    const third = await client.fetchAgentTimeline(agent.id, {
-      direction: "after",
-      cursor: second.endCursor!,
-    });
-    expect(second.entries).toHaveLength(200);
-    expect(third.entries).toHaveLength(51);
-    expect(third.hasNewer).toBe(false);
-    expect(
-      [...first.entries, ...second.entries, ...third.entries].map((entry) => entry.item),
-    ).toEqual(
-      Array.from({ length: 451 }, (_, index) => ({ type: "user_message", text: String(index) })),
-    );
-    const allAfter = await client.fetchAgentTimeline(agent.id, {
-      direction: "after",
-      cursor,
-      limit: 0,
-    });
-    const allTail = await client.fetchAgentTimeline(agent.id, { direction: "tail", limit: 0 });
-    expect(allAfter.entries).toHaveLength(451);
-    expect(allAfter.hasNewer).toBe(false);
-    expect(allTail.entries).toHaveLength(initial.entries.length + 451);
-  } finally {
-    await client.close();
-    await daemon.close();
-  }
-}, 60_000);

packages/server/src/server/session.ts

@@ -7787,6 +7787,8 @@ export class Session {
   ): Promise<void> {
     const direction: AgentTimelineFetchDirection = msg.direction ?? (msg.cursor ? "after" : "tail");
     const projection = "projected" as const;
+    const requestedLimit = msg.limit;
+    const pageLimit = requestedLimit ?? (direction === "after" ? 0 : 200);
     const cursor: AgentTimelineCursor | undefined = msg.cursor
       ? {
           epoch: msg.cursor.epoch,
@@ -7805,7 +7807,7 @@ export class Session {
       const fetchedControlTimeline = this.agentManager.fetchTimeline(msg.agentId, {
         direction,
         cursor,
-        limit: msg.limit,
+        limit: pageLimit,
       });
       const selectedTimeline = {
         timeline: fetchedControlTimeline,

packages/server/src/server/websocket-server.ts

@@ -358,7 +358,7 @@ function createNoopWorkspaceRegistry(): WorkspaceRegistry {
     get: async () => null,
     update: async () => null,
     upsert: async () => {},
-    archive: async () => {},
+    archive: async () => false,
     remove: async () => {},
   };
 }

packages/server/src/server/workspace-reconciliation-observation.test.ts

@@ -495,6 +495,10 @@ describe("observed workspace placement", () => {
 
     expect((await observed.placement("workspace-one"))?.archivedAt).toEqual(expect.any(String));
     expect(observed.workspaceBatches).toEqual([["workspace-one"]]);
+    const archived = await observed.placement("workspace-one");
+    await observed.advanceBy(RESCAN_INTERVAL_MS);
+    expect(await observed.placement("workspace-one")).toEqual(archived);
+    expect(observed.workspaceBatches).toEqual([["workspace-one"]]);
     observed.dispose();
   });
 

packages/server/src/server/workspace-reconciliation-service.test.ts

@@ -31,6 +31,14 @@ function canonicalLocalProjectKey(rootPath: string): string {
 }
 
 function createTestRegistries() {
+  let archiveGate: {
+    started: ReturnType<typeof deferred>;
+    release: ReturnType<typeof deferred>;
+  } | null = null;
+  const holdNextArchive = () => {
+    archiveGate = { started: deferred(), release: deferred() };
+    return archiveGate;
+  };
   const projects = new Map<string, PersistedProjectRecord>();
   const workspaces = new Map<string, PersistedWorkspaceRecord>();
 
@@ -55,6 +63,13 @@ function createTestRegistries() {
       projects.set(record.projectId, record);
       return record;
     },
+    update: async (id, updater) => {
+      const current = projects.get(id);
+      if (!current) return null;
+      const updated = updater(current);
+      projects.set(id, updated);
+      return updated;
+    },
     upsert: async (record: PersistedProjectRecord) => {
       projects.set(record.projectId, record);
     },
@@ -85,17 +100,23 @@ function createTestRegistries() {
       workspaces.set(record.workspaceId, record);
     },
     archive: async (id: string, archivedAt: string) => {
-      const existing = workspaces.get(id);
-      if (existing) {
-        workspaces.set(id, { ...existing, archivedAt, updatedAt: archivedAt });
+      const gate = archiveGate;
+      archiveGate = null;
+      if (gate) {
+        gate.started.resolve();
+        await gate.release.promise;
       }
+      const existing = workspaces.get(id);
+      if (!existing || existing.archivedAt) return false;
+      workspaces.set(id, { ...existing, archivedAt, updatedAt: archivedAt });
+      return true;
     },
     remove: async (id: string) => {
       workspaces.delete(id);
     },
   };
 
-  return { projects, workspaces, projectRegistry, workspaceRegistry };
+  return { projects, workspaces, projectRegistry, workspaceRegistry, holdNextArchive };
 }
 
 function createTestLogger() {
@@ -117,6 +138,7 @@ interface CapturedLogRecord {
 
 function createCapturingLogger() {
   const infoRecords: CapturedLogRecord[] = [];
+  const warnRecords: CapturedLogRecord[] = [];
   const logger = {
     child: () => logger,
     trace: () => undefined,
@@ -124,10 +146,12 @@ function createCapturingLogger() {
     info: (payload: unknown, message?: string) => {
       infoRecords.push({ payload, message: message ?? "" });
     },
-    warn: () => undefined,
+    warn: (payload: unknown, message?: string) => {
+      warnRecords.push({ payload, message: message ?? "" });
+    },
     error: () => undefined,
   };
-  return { logger: logger as unknown as pino.Logger, infoRecords };
+  return { logger: logger as unknown as pino.Logger, infoRecords, warnRecords };
 }
 
 function createWorkspaceGitServiceStub(
@@ -241,6 +265,419 @@ describe("WorkspaceReconciliationService", () => {
     tempDirs.length = 0;
   });
 
+  test("does not emit a duplicate archive when user archival commits before reconciliation's archive", async () => {
+    const rootPath = realpathSync(mkdtempSync(path.join(tmpdir(), "reconcile-archive-commit-")));
+    tempDirs.push(rootPath);
+    const { projects, workspaces, projectRegistry, workspaceRegistry, holdNextArchive } =
+      createTestRegistries();
+    projects.set(
+      "p1",
+      createPersistedProjectRecord({
+        projectId: "p1",
+        rootPath,
+        projectKey: canonicalLocalProjectKey(rootPath),
+        kind: "non_git",
+        displayName: "project",
+        createdAt: timestamp,
+        updatedAt: timestamp,
+      }),
+    );
+    workspaces.set(
+      "w1",
+      createPersistedWorkspaceRecord({
+        workspaceId: "w1",
+        projectId: "p1",
+        cwd: path.join(rootPath, "missing"),
+        kind: "directory",
+        displayName: "workspace",
+        createdAt: timestamp,
+        updatedAt: timestamp,
+      }),
+    );
+    const callbacks: string[] = [];
+    const service = new WorkspaceReconciliationService({
+      projectRegistry,
+      workspaceRegistry,
+      logger: createTestLogger(),
+      onWorkspaceArchived: (id) => {
+        callbacks.push(id);
+      },
+    });
+    const gate = holdNextArchive();
+    try {
+      const scan = service.runOnce();
+      await gate.started.promise;
+      expect(await workspaceRegistry.archive("w1", timestamp)).toBe(true);
+      gate.release.resolve();
+      expect((await scan).changesApplied).toEqual([]);
+      expect(callbacks).toEqual([]);
+      expect(workspaces.get("w1")?.archivedAt).toBe(timestamp);
+    } finally {
+      gate.release.resolve();
+      service.dispose();
+    }
+  });
+
+  test("preserves paths while two inspections saturate capacity, logs once, and recovers after they drain", async () => {
+    const rootPath = realpathSync(mkdtempSync(path.join(tmpdir(), "reconcile-saturated-")));
+    tempDirs.push(rootPath);
+    const { projects, workspaces, projectRegistry, workspaceRegistry } = createTestRegistries();
+    const { logger, warnRecords, infoRecords } = createCapturingLogger();
+    projects.set(
+      "p1",
+      createPersistedProjectRecord({
+        projectId: "p1",
+        rootPath,
+        projectKey: canonicalLocalProjectKey(rootPath),
+        kind: "non_git",
+        displayName: "project",
+        createdAt: timestamp,
+        updatedAt: timestamp,
+      }),
+    );
+    const ids = ["hung1", "hung2", "healthy"];
+    for (const workspaceId of ids) {
+      workspaces.set(
+        workspaceId,
+        createPersistedWorkspaceRecord({
+          workspaceId,
+          projectId: "p1",
+          cwd: path.join(rootPath, workspaceId),
+          kind: "directory",
+          displayName: workspaceId,
+          createdAt: timestamp,
+          updatedAt: timestamp,
+        }),
+      );
+    }
+    const release = deferred();
+    const calls: string[] = [];
+    let recovered = false;
+    let ticks = 0;
+    const probe = setInterval(() => ticks++, 1);
+    const service = new WorkspaceReconciliationService({
+      projectRegistry,
+      workspaceRegistry,
+      logger,
+      inspectionTimeoutMs: 30,
+      inspectDirectory: async (targetPath) => {
+        calls.push(targetPath);
+        if (!recovered && path.basename(targetPath).startsWith("hung")) await release.promise;
+        return "directory";
+      },
+    });
+    try {
+      const result = await service.runOnce();
+      expect(ticks).toBeGreaterThan(0);
+      expect(result.durationMs).toBeLessThan(1000);
+      expect(result.changesApplied).toEqual([]);
+      expect(calls).toEqual(ids.slice(0, 2).map((id) => path.join(rootPath, id)));
+      expect([...workspaces.values()].map((workspace) => workspace.archivedAt)).toEqual([
+        null,
+        null,
+        null,
+      ]);
+      expect(warnRecords.filter((record) => record.message.includes("saturated"))).toEqual([
+        {
+          message: "Workspace directory inspection saturated; preserving uninspected workspaces",
+          payload: { paths: ids.slice(0, 2).map((id) => path.join(rootPath, id)) },
+        },
+      ]);
+      recovered = true;
+      release.resolve();
+      await new Promise<void>((resolve) => setImmediate(resolve));
+      expect(infoRecords).toEqual([
+        {
+          message:
+            "Timed-out workspace directory inspections drained; reconciliation capacity restored",
+          payload: {},
+        },
+      ]);
+      calls.length = 0;
+      await service.runOnce();
+      expect(calls).toEqual([...ids.map((id) => path.join(rootPath, id)), rootPath]);
+      expect(warnRecords.filter((record) => record.message.includes("saturated"))).toHaveLength(1);
+    } finally {
+      release.resolve();
+      clearInterval(probe);
+      service.dispose();
+    }
+  });
+
+  test("inspects every healthy path when one hung inspection times out during a longer scan", async () => {
+    const rootPath = realpathSync(mkdtempSync(path.join(tmpdir(), "reconcile-long-hung-")));
+    tempDirs.push(rootPath);
+    const { projects, workspaces, projectRegistry, workspaceRegistry } = createTestRegistries();
+    projects.set(
+      "p1",
+      createPersistedProjectRecord({
+        projectId: "p1",
+        rootPath,
+        projectKey: canonicalLocalProjectKey(rootPath),
+        kind: "non_git",
+        displayName: "project",
+        createdAt: timestamp,
+        updatedAt: timestamp,
+      }),
+    );
+    const healthyIds = Array.from({ length: 12 }, (_, i) => `healthy${i}`);
+    for (const workspaceId of ["hung", ...healthyIds]) {
+      workspaces.set(
+        workspaceId,
+        createPersistedWorkspaceRecord({
+          workspaceId,
+          projectId: "p1",
+          cwd: path.join(rootPath, workspaceId),
+          kind: "directory",
+          displayName: workspaceId,
+          createdAt: timestamp,
+          updatedAt: timestamp,
+        }),
+      );
+    }
+    const calls: string[] = [];
+    let outstanding = 0;
+    let maximumOutstanding = 0;
+    const { logger, warnRecords } = createCapturingLogger();
+    const service = new WorkspaceReconciliationService({
+      projectRegistry,
+      workspaceRegistry,
+      logger,
+      inspectionTimeoutMs: 100,
+      inspectDirectory: async (targetPath) => {
+        calls.push(targetPath);
+        maximumOutstanding = Math.max(maximumOutstanding, ++outstanding);
+        if (path.basename(targetPath) === "hung") return new Promise(() => {});
+        await new Promise<void>((resolve) => setTimeout(resolve, 20));
+        outstanding--;
+        return "directory";
+      },
+    });
+    try {
+      const result = await service.runOnce();
+      expect(result.durationMs).toBeGreaterThan(100);
+      expect(calls).toEqual(
+        ["hung", ...healthyIds].map((id) => path.join(rootPath, id)).concat(rootPath),
+      );
+      expect(maximumOutstanding).toBe(2);
+      expect(outstanding).toBe(1);
+      expect(workspaces.get("hung")?.archivedAt).toBeNull();
+      expect(result.changesApplied).toEqual([]);
+      expect(warnRecords.filter((record) => record.message.includes("saturated"))).toEqual([]);
+    } finally {
+      service.dispose();
+    }
+  });
+
+  test("times out a hung inspection without archiving it or blocking healthy paths, and retains its IO slot", async () => {
+    const rootPath = realpathSync(mkdtempSync(path.join(tmpdir(), "reconcile-hung-")));
+    tempDirs.push(rootPath);
+    const { projects, workspaces, projectRegistry, workspaceRegistry } = createTestRegistries();
+    projects.set(
+      "p1",
+      createPersistedProjectRecord({
+        projectId: "p1",
+        rootPath,
+        projectKey: canonicalLocalProjectKey(rootPath),
+        kind: "non_git",
+        displayName: "project",
+        createdAt: timestamp,
+        updatedAt: timestamp,
+      }),
+    );
+    for (const workspaceId of ["hung", "healthy", "healthy2", "healthy3"]) {
+      workspaces.set(
+        workspaceId,
+        createPersistedWorkspaceRecord({
+          workspaceId,
+          projectId: "p1",
+          cwd: path.join(rootPath, workspaceId),
+          kind: "directory",
+          displayName: workspaceId,
+          createdAt: timestamp,
+          updatedAt: timestamp,
+        }),
+      );
+    }
+    const calls: string[] = [];
+    let outstanding = 0;
+    let maximumOutstanding = 0;
+    const healthyInspected = deferred();
+    const service = new WorkspaceReconciliationService({
+      projectRegistry,
+      workspaceRegistry,
+      logger: createTestLogger(),
+      inspectionTimeoutMs: 30,
+      inspectDirectory: async (targetPath) => {
+        calls.push(targetPath);
+        maximumOutstanding = Math.max(maximumOutstanding, ++outstanding);
+        if (path.basename(targetPath) === "hung") return new Promise(() => {});
+        healthyInspected.resolve();
+        await new Promise<void>((resolve) => setImmediate(resolve));
+        outstanding--;
+        return "directory";
+      },
+    });
+    try {
+      const scan = service.runOnce();
+      await Promise.race([
+        healthyInspected.promise,
+        scan.then(() => {
+          throw new Error("Reconciliation did not use its directory inspection capability");
+        }),
+      ]);
+      expect(outstanding).toBeLessThanOrEqual(2);
+      expect(workspaces.get("hung")?.archivedAt).toBeNull();
+      const result = await scan;
+      expect(result.changesApplied).toEqual([]);
+      await service.runOnce();
+      expect(calls.filter((cwd) => path.basename(cwd) === "hung")).toHaveLength(1);
+      expect(calls.filter((cwd) => path.basename(cwd) === "healthy3")).toHaveLength(2);
+      expect(maximumOutstanding).toBe(2);
+      expect([...workspaces.values()].map((workspace) => workspace.archivedAt)).toEqual([
+        null,
+        null,
+        null,
+        null,
+      ]);
+    } finally {
+      service.dispose();
+    }
+  });
+
+  test.each(["missing", "directory"] as const)(
+    "does not process or archive a workspace archived during %s inspection",
+    async (state) => {
+      const rootPath = realpathSync(
+        mkdtempSync(path.join(tmpdir(), "reconcile-inspection-archive-")),
+      );
+      tempDirs.push(rootPath);
+      const { projects, workspaces, projectRegistry, workspaceRegistry } = createTestRegistries();
+      projects.set(
+        "p1",
+        createPersistedProjectRecord({
+          projectId: "p1",
+          rootPath,
+          projectKey: canonicalLocalProjectKey(rootPath),
+          kind: "non_git",
+          displayName: "project",
+          createdAt: timestamp,
+          updatedAt: timestamp,
+        }),
+      );
+      const cwd = path.join(rootPath, "missing");
+      workspaces.set(
+        "w1",
+        createPersistedWorkspaceRecord({
+          workspaceId: "w1",
+          projectId: "p1",
+          cwd,
+          kind: "directory",
+          displayName: "workspace",
+          createdAt: timestamp,
+          updatedAt: timestamp,
+        }),
+      );
+      const started = deferred();
+      const release = deferred();
+      const archivedCallbacks: string[] = [];
+      const checkouts = new TestCheckouts();
+      const service = new WorkspaceReconciliationService({
+        projectRegistry,
+        workspaceRegistry,
+        logger: createTestLogger(),
+        workspaceGitService: checkouts,
+        onWorkspaceArchived: (id) => {
+          archivedCallbacks.push(id);
+        },
+        inspectDirectory: async (targetPath) => {
+          if (targetPath === cwd) {
+            started.resolve();
+            await release.promise;
+            return state;
+          }
+          return "directory";
+        },
+      });
+      try {
+        const scan = service.runOnce();
+        await Promise.race([
+          started.promise,
+          scan.then(() => {
+            throw new Error("Reconciliation did not use its directory inspection capability");
+          }),
+        ]);
+        await workspaceRegistry.archive("w1", "2026-01-01T00:00:00.000Z");
+        const archived = workspaces.get("w1");
+        release.resolve();
+        const result = await scan;
+        expect(workspaces.get("w1")).toEqual(archived);
+        expect(archivedCallbacks).toEqual([]);
+        expect(checkouts.reads).toEqual([rootPath]);
+        expect(result.changesApplied).toEqual([]);
+      } finally {
+        release.resolve();
+        service.dispose();
+      }
+    },
+  );
+
+  test("keeps the event loop responsive while inspecting 20000 real workspace paths", async () => {
+    const rootPath = realpathSync(mkdtempSync(path.join(tmpdir(), "reconcile-many-")));
+    tempDirs.push(rootPath);
+    const { projects, workspaces, projectRegistry, workspaceRegistry } = createTestRegistries();
+    projects.set(
+      "p1",
+      createPersistedProjectRecord({
+        projectId: "p1",
+        rootPath,
+        projectKey: canonicalLocalProjectKey(rootPath),
+        kind: "non_git",
+        displayName: "project",
+        createdAt: timestamp,
+        updatedAt: timestamp,
+      }),
+    );
+    for (let i = 0; i < 20000; i++) {
+      const workspaceId = `w${i}`;
+      workspaces.set(
+        workspaceId,
+        createPersistedWorkspaceRecord({
+          workspaceId,
+          projectId: "p1",
+          cwd: path.join(rootPath, workspaceId),
+          kind: "directory",
+          displayName: workspaceId,
+          createdAt: timestamp,
+          updatedAt: timestamp,
+        }),
+      );
+    }
+    const service = new WorkspaceReconciliationService({
+      projectRegistry,
+      workspaceRegistry,
+      logger: createTestLogger(),
+    });
+    let last = performance.now();
+    let longestGap = 0;
+    const probe = setInterval(() => {
+      const now = performance.now();
+      longestGap = Math.max(longestGap, now - last);
+      last = now;
+    }, 1);
+    let result;
+    try {
+      result = await service.runOnce();
+      await new Promise<void>((resolve) => setTimeout(resolve, 1));
+    } finally {
+      clearInterval(probe);
+      service.dispose();
+    }
+    expect(longestGap).toBeLessThan(20);
+    expect(result.changesApplied).toHaveLength(20000);
+    expect([...workspaces.values()].every((workspace) => workspace.archivedAt !== null)).toBe(true);
+  }, 30000);
+
   test("preserves workspace archival that lands during boot reconciliation", async () => {
     const workspaceRoot = realpathSync(mkdtempSync(path.join(tmpdir(), "reconcile-archive-race-")));
     tempDirs.push(workspaceRoot);

packages/server/src/server/workspace-reconciliation-service.ts

@@ -1,4 +1,6 @@
-import { statSync, watch as watchPath } from "node:fs";
+import { watch as watchPath } from "node:fs";
+import { stat } from "node:fs/promises";
+import { setImmediate as yieldToLoop } from "node:timers/promises";
 import type { ProjectCheckoutLitePayload } from "@getpaseo/protocol/messages";
 import type pino from "pino";
 import type {
@@ -19,6 +21,8 @@ import { deriveProjectKey } from "./project-key.js";
 
 const DEFAULT_RESCAN_INTERVAL_MS = 5 * 60_000;
 const DEFAULT_DEBOUNCE_MS = 100;
+const INSPECTION_CONCURRENCY = 2;
+const DEFAULT_INSPECTION_TIMEOUT_MS = 5000;
 
 export type ProjectUpdate =
   | { kind: "upsert"; project: PersistedProjectRecord }
@@ -95,6 +99,8 @@ export interface WorkspaceReconciliationServiceOptions {
   clock?: ReconciliationClock;
   rescanIntervalMs?: number;
   debounceMs?: number;
+  inspectDirectory?: (targetPath: string) => Promise<DirectoryState>;
+  inspectionTimeoutMs?: number;
 }
 
 interface ProjectReconciliationInput {
@@ -110,9 +116,17 @@ interface CachedCheckoutRead {
   checkout: Promise<ProjectCheckoutLitePayload>;
 }
 
-type DirectoryState = "directory" | "missing" | "unreadable";
+export type DirectoryState = "directory" | "missing" | "unreadable";
 
 export class WorkspaceReconciliationService {
+  // Timed-out fs operations retain their slot until the OS returns. Never use
+  // the deadline to admit more work into libuv's shared threadpool.
+  private readonly timedOutPaths = new Set<string>();
+  private inspectionSaturated = false;
+  private readonly inspectionWaiters = new Set<() => void>();
+  private readonly pendingInspections = new Map<string, Promise<DirectoryState>>();
+  private readonly directoryInspection: (targetPath: string) => Promise<DirectoryState>;
+  private readonly inspectionTimeoutMs: number;
   private readonly serverId: string | undefined;
   private readonly projectRegistry: ProjectRegistry;
   private readonly workspaceRegistry: WorkspaceRegistry;
@@ -136,6 +150,10 @@ export class WorkspaceReconciliationService {
   private reconcileQueuedMode: "metadata" | "full" | null = null;
 
   constructor(options: WorkspaceReconciliationServiceOptions) {
+    this.directoryInspection =
+      options.inspectDirectory ??
+      (async (targetPath) => ((await stat(targetPath)).isDirectory() ? "directory" : "missing"));
+    this.inspectionTimeoutMs = options.inspectionTimeoutMs ?? DEFAULT_INSPECTION_TIMEOUT_MS;
     this.serverId = options.serverId;
     this.projectRegistry = options.projectRegistry;
     this.workspaceRegistry = options.workspaceRegistry;
@@ -180,6 +198,7 @@ export class WorkspaceReconciliationService {
 
   dispose(): void {
     this.disposed = true;
+    this.wakeInspectionWaiters();
     this.unsubscribeRegistry?.();
     this.unsubscribeRegistry = null;
     if (this.rescanTimer) this.clock.clearInterval(this.rescanTimer);
@@ -197,16 +216,23 @@ export class WorkspaceReconciliationService {
       this.workspaceRegistry.list(),
     ]);
     const workspacesByProject = new Map<string, PersistedWorkspaceRecord[]>();
-    for (const workspace of workspaces) {
-      if (workspace.archivedAt || this.inspectDirectory(workspace.cwd) !== "directory") continue;
+    const workspaceStates = await mapBounded(
+      workspaces.filter((w) => !w.archivedAt),
+      async (workspace) => ({ workspace, state: await this.inspectDirectory(workspace.cwd) }),
+    );
+    for (const { workspace, state } of workspaceStates) {
+      if (state !== "directory") continue;
+      if ((await this.workspaceRegistry.get(workspace.workspaceId))?.archivedAt !== null) continue;
       const siblings = workspacesByProject.get(workspace.projectId) ?? [];
       siblings.push(workspace);
       workspacesByProject.set(workspace.projectId, siblings);
     }
+    const projectStates = await mapBounded(
+      projects.filter((p) => !p.archivedAt),
+      async (project) => ({ project, state: await this.inspectDirectory(project.rootPath) }),
+    );
     await this.reconcileGitMetadataForProjects(
-      projects.filter(
-        (project) => !project.archivedAt && this.inspectDirectory(project.rootPath) === "directory",
-      ),
+      projectStates.filter(({ state }) => state === "directory").map(({ project }) => project),
       workspacesByProject,
       changes,
     );
@@ -222,23 +248,30 @@ export class WorkspaceReconciliationService {
     const allWorkspaces = await this.workspaceRegistry.list();
 
     const activeProjects = allProjects.filter((p) => !p.archivedAt);
+    const activeProjectsById = new Map(
+      activeProjects.map((project) => [project.projectId, project]),
+    );
     const activeWorkspaces = allWorkspaces.filter((w) => !w.archivedAt);
-    const workspaceDirectoryStates = activeWorkspaces.map((workspace) => ({
+    const workspaceDirectoryStates = await mapBounded(activeWorkspaces, async (workspace) => ({
       workspace,
-      state: this.inspectDirectory(workspace.cwd),
+      state: await this.inspectDirectory(workspace.cwd),
+    }));
+    // Read project roots after workspaces: losing a volume can withhold an
+    // archive, never turn a workspace's absence into proof of deletion.
+    const projectStates = await mapBounded(activeProjects, async (project) => ({
+      project,
+      state: await this.inspectDirectory(project.rootPath),
     }));
-    // Project roots are read after the workspace directories, so a volume that
-    // goes away mid-pass leaves its project unreachable rather than its workspaces
-    // alone. The skew can only withhold an archive, never produce one.
     const reachableProjectIds = new Set(
-      activeProjects
-        .filter((project) => this.inspectDirectory(project.rootPath) === "directory")
-        .map((project) => project.projectId),
+      projectStates
+        .filter(({ state }) => state === "directory")
+        .map(({ project }) => project.projectId),
     );
 
     const workspacesByProject = new Map<string, PersistedWorkspaceRecord[]>();
     for (const { workspace, state } of workspaceDirectoryStates) {
       if (state !== "directory") continue;
+      if ((await this.workspaceRegistry.get(workspace.workspaceId))?.archivedAt !== null) continue;
       const list = workspacesByProject.get(workspace.projectId) ?? [];
       list.push(workspace);
       workspacesByProject.set(workspace.projectId, list);
@@ -255,26 +288,29 @@ export class WorkspaceReconciliationService {
           state === "missing" && reachableProjectIds.has(workspace.projectId),
       )
       .map(({ workspace }) => workspace);
-    await Promise.all(
-      missingWorkspaces.map(async (workspace) => {
-        const timestamp = new Date().toISOString();
-        await this.workspaceRegistry.archive(workspace.workspaceId, timestamp);
-        await this.onWorkspaceArchived?.(workspace.workspaceId);
-        changes.push({
-          kind: "workspace_archived",
-          workspaceId: workspace.workspaceId,
-          directory: workspace.cwd,
-          reason: "directory_missing",
-        });
-
-        // Update the in-memory list for the project orphan check below
-        const siblings = workspacesByProject.get(workspace.projectId);
-        if (siblings) {
-          const updated = siblings.filter((w) => w.workspaceId !== workspace.workspaceId);
-          workspacesByProject.set(workspace.projectId, updated);
-        }
-      }),
-    );
+    await mapBounded(missingWorkspaces, async (workspace) => {
+      const current = await this.workspaceRegistry.get(workspace.workspaceId);
+      const project = await this.projectRegistry.get(workspace.projectId);
+      if (
+        !current ||
+        current.archivedAt ||
+        current.cwd !== workspace.cwd ||
+        current.projectId !== workspace.projectId ||
+        !project ||
+        project.archivedAt ||
+        project.rootPath !== activeProjectsById.get(project.projectId)?.rootPath
+      )
+        return;
+      const timestamp = new Date().toISOString();
+      if (!(await this.workspaceRegistry.archive(workspace.workspaceId, timestamp))) return;
+      await this.onWorkspaceArchived?.(workspace.workspaceId);
+      changes.push({
+        kind: "workspace_archived",
+        workspaceId: workspace.workspaceId,
+        directory: workspace.cwd,
+        reason: "directory_missing",
+      });
+    });
 
     // 2. Reconcile mutable git metadata without changing identity or membership.
     //    Projects persist until explicitly removed, even when they currently have
@@ -351,13 +387,17 @@ export class WorkspaceReconciliationService {
   }
 
   private async reconcileProject(input: ProjectReconciliationInput): Promise<void> {
-    const { project, siblings, currentGit, readCheckout, changes } = input;
+    const { siblings, currentGit, readCheckout, changes } = input;
     const workspaceCheckouts = await Promise.all(
-      siblings.map(async (workspace) => ({
-        workspace,
-        checkout: await readCheckout(workspace.cwd),
-      })),
+      siblings.map(async (workspace) => {
+        const current = await this.workspaceRegistry.get(workspace.workspaceId);
+        if (!current || current.cwd !== workspace.cwd || current.projectId !== workspace.projectId)
+          return null;
+        return { workspace: current, checkout: await readCheckout(current.cwd) };
+      }),
     );
+    const project = await this.projectRegistry.get(input.project.projectId);
+    if (!project || project.archivedAt || project.rootPath !== input.project.rootPath) return;
     const projectUpdates: Partial<Pick<PersistedProjectRecord, "kind" | "projectKey">> = {};
     const mappedKind = deriveProjectKind(currentGit);
     const projectKey = deriveProjectKey({
@@ -377,40 +417,47 @@ export class WorkspaceReconciliationService {
 
     if (Object.keys(projectUpdates).length > 0) {
       const timestamp = new Date().toISOString();
-      await this.projectRegistry.upsert({
-        ...project,
-        ...projectUpdates,
-        updatedAt: timestamp,
-      });
-      changes.push({
-        kind: "project_updated",
-        projectId: project.projectId,
-        directory: project.rootPath,
-        fields: projectUpdates,
+      let applied = false;
+      await this.projectRegistry.update(project.projectId, (current) => {
+        if (current.archivedAt || current.rootPath !== project.rootPath) return current;
+        applied = true;
+        return { ...current, ...projectUpdates, updatedAt: timestamp };
       });
+      if (applied)
+        changes.push({
+          kind: "project_updated",
+          projectId: project.projectId,
+          directory: project.rootPath,
+          fields: projectUpdates,
+        });
     }
 
     await Promise.all(
-      workspaceCheckouts.map(async ({ workspace, checkout: wsGit }) => {
+      workspaceCheckouts.map(async (entry) => {
+        if (!entry) return;
+        const { workspace, checkout: wsGit } = entry;
         const timestamp = new Date().toISOString();
-        const update = reconcileWorkspacePlacement({
-          workspace,
-          checkout: wsGit,
-          updatedAt: timestamp,
+        if (!reconcileWorkspacePlacement({ workspace, checkout: wsGit, updatedAt: timestamp }))
+          return;
+        let fields: Partial<MutableWorkspacePlacement> | null = null;
+        await this.workspaceRegistry.update(workspace.workspaceId, (current) => {
+          if (current.cwd !== workspace.cwd || current.projectId !== workspace.projectId)
+            return current;
+          const update = reconcileWorkspacePlacement({
+            workspace: current,
+            checkout: wsGit,
+            updatedAt: timestamp,
+          });
+          if (!update) return current;
+          fields = update.fields;
+          return { ...current, ...fields, updatedAt: timestamp };
         });
-        if (!update) return;
-
-        const updated = await this.workspaceRegistry.update(workspace.workspaceId, (current) => ({
-          ...current,
-          ...update.fields,
-          updatedAt: timestamp,
-        }));
-        if (!updated) return;
+        if (!fields) return;
         changes.push({
           kind: "workspace_updated",
           workspaceId: workspace.workspaceId,
           directory: workspace.cwd,
-          fields: update.fields,
+          fields,
         });
       }),
     );
@@ -537,16 +584,74 @@ export class WorkspaceReconciliationService {
     return this.workspaceGitService.getCheckout(cwd);
   }
 
-  private inspectDirectory(targetPath: string): DirectoryState {
+  private wakeInspectionWaiters(): void {
+    for (const wake of this.inspectionWaiters) wake();
+    this.inspectionWaiters.clear();
+  }
+
+  private async inspectDirectory(targetPath: string): Promise<DirectoryState> {
+    // A healthy in-flight inspection owns capacity temporarily. Wait for it;
+    // only unresolved operations that have all timed out justify skipping paths.
+    while (
+      !this.disposed &&
+      !this.pendingInspections.has(targetPath) &&
+      this.pendingInspections.size >= INSPECTION_CONCURRENCY
+    ) {
+      if (this.timedOutPaths.size === INSPECTION_CONCURRENCY) return "unreadable";
+      await new Promise<void>((resolve) => this.inspectionWaiters.add(resolve));
+    }
+    if (this.disposed) return "unreadable";
+    let pending = this.pendingInspections.get(targetPath);
+    if (!pending) {
+      pending = Promise.resolve()
+        .then(() => this.directoryInspection(targetPath))
+        .catch((error) => {
+          if (isMissingPathError(error)) return "missing" as const;
+          this.logger.warn(
+            { err: error, targetPath },
+            "Skipped workspace reconciliation after directory inspection failed",
+          );
+          return "unreadable" as const;
+        })
+        .finally(() => {
+          this.pendingInspections.delete(targetPath);
+          this.timedOutPaths.delete(targetPath);
+          this.wakeInspectionWaiters();
+          if (this.inspectionSaturated && this.timedOutPaths.size === 0) {
+            this.inspectionSaturated = false;
+            this.logger.info(
+              {},
+              "Timed-out workspace directory inspections drained; reconciliation capacity restored",
+            );
+          }
+        });
+      this.pendingInspections.set(targetPath, pending);
+    }
+    let timer: ReturnType<typeof setTimeout> | undefined;
     try {
-      return statSync(targetPath).isDirectory() ? "directory" : "missing";
-    } catch (error) {
-      if (isMissingPathError(error)) return "missing";
-      this.logger.warn(
-        { err: error, targetPath },
-        "Skipped workspace reconciliation after directory inspection failed",
-      );
-      return "unreadable";
+      return await Promise.race([
+        pending,
+        new Promise<DirectoryState>((resolve) => {
+          timer = setTimeout(() => {
+            this.timedOutPaths.add(targetPath);
+            this.wakeInspectionWaiters();
+            if (!this.inspectionSaturated && this.timedOutPaths.size === INSPECTION_CONCURRENCY) {
+              this.inspectionSaturated = true;
+              this.logger.warn(
+                { paths: [...this.timedOutPaths] },
+                "Workspace directory inspection saturated; preserving uninspected workspaces",
+              );
+            }
+            this.logger.warn(
+              { targetPath },
+              "Skipped workspace reconciliation after directory inspection timed out",
+            );
+            resolve("unreadable");
+          }, this.inspectionTimeoutMs);
+        }),
+      ]);
+    } finally {
+      clearTimeout(timer);
     }
   }
 }
@@ -555,3 +660,21 @@ function isMissingPathError(error: unknown): boolean {
   if (typeof error !== "object" || error === null || !("code" in error)) return false;
   return error.code === "ENOENT" || error.code === "ENOTDIR";
 }
+
+// Two workers bound admission; yielding also bounds passes whose adapters settle
+// immediately (including unavailable paths after both IO slots time out).
+async function mapBounded<T, R>(items: T[], visit: (item: T) => Promise<R>): Promise<R[]> {
+  const results: R[] = [];
+  let next = 0;
+  await Promise.all(
+    Array.from({ length: Math.min(INSPECTION_CONCURRENCY, items.length) }, async () => {
+      let count = 0;
+      while (next < items.length) {
+        const index = next++;
+        results[index] = await visit(items[index]!);
+        if (++count % 32 === 0) await yieldToLoop();
+      }
+    }),
+  );
+  return results;
+}

packages/server/src/server/workspace-registry.test.ts

@@ -474,7 +474,7 @@ describe("workspace registries", () => {
     expect(await workspaceRegistry.list()).toEqual([]);
   });
 
-  test("refreshes workspace archive timestamps when an archive is repeated", async () => {
+  test("preserves the first workspace archive and reports whether a queued archive applied", async () => {
     await workspaceRegistry.initialize();
     await workspaceRegistry.upsert(
       createPersistedWorkspaceRecord({
@@ -488,12 +488,24 @@ describe("workspace registries", () => {
       }),
     );
 
-    await workspaceRegistry.archive("workspace-one", "2026-03-02T00:00:00.000Z");
-    await workspaceRegistry.archive("workspace-one", "2026-03-03T00:00:00.000Z");
-
-    expect(await workspaceRegistry.get("workspace-one")).toMatchObject({
-      archivedAt: "2026-03-03T00:00:00.000Z",
-      updatedAt: "2026-03-03T00:00:00.000Z",
+    const events: WorkspaceMutation[] = [];
+    workspaceRegistry.subscribeToMutations((event) => {
+      events.push(event);
+    });
+    expect(
+      await Promise.all([
+        workspaceRegistry.archive("workspace-one", "2026-03-02T00:00:00.000Z"),
+        workspaceRegistry.archive("workspace-one", "2026-03-03T00:00:00.000Z"),
+      ]),
+    ).toEqual([true, false]);
+    expect(events.map((event) => event.kind)).toEqual(["archive"]);
+    const reloaded = new FileBackedWorkspaceRegistry(
+      path.join(tmpDir, "projects", "workspaces.json"),
+      logger,
+    );
+    expect(await reloaded.get("workspace-one")).toMatchObject({
+      archivedAt: "2026-03-02T00:00:00.000Z",
+      updatedAt: "2026-03-02T00:00:00.000Z",
     });
   });
 

packages/server/src/server/workspace-registry.ts

@@ -167,7 +167,7 @@ export interface WorkspaceRegistry {
     workspaceId: string,
     archivedAt: string,
     context?: WorkspaceArchiveContext,
-  ): Promise<void>;
+  ): Promise<boolean>;
   remove(workspaceId: string): Promise<void>;
   /** Central lifecycle seam for daemon-global workspace observers. */
   subscribeToMutations?(
@@ -247,20 +247,6 @@ class FileBackedRegistry<TRecord extends RegistryRecord> {
     });
   }
 
-  async archive(id: string, archivedAt: string): Promise<void> {
-    await this.archiveIfPresent(id, archivedAt);
-  }
-
-  protected async archiveIfPresent(id: string, archivedAt: string): Promise<TRecord | null> {
-    return this.mutateCache((records) => {
-      const existing = records.get(id);
-      if (!existing) return null;
-      const next = this.schema.parse({ ...existing, updatedAt: archivedAt, archivedAt });
-      records.set(id, next);
-      return next;
-    });
-  }
-
   protected async archiveIfActive(id: string, archivedAt: string): Promise<TRecord | null> {
     return this.mutateCache((records) => {
       const existing = records.get(id);
@@ -485,7 +471,7 @@ export class FileBackedProjectRegistry
     return project;
   }
 
-  override async archive(projectId: string, archivedAt: string): Promise<void> {
+  async archive(projectId: string, archivedAt: string): Promise<void> {
     const project = await this.archiveIfActive(projectId, archivedAt);
     if (!project) return;
     await this.notifyMutation({ kind: "archive", projectId, project });
@@ -565,21 +551,28 @@ export class FileBackedWorkspaceRegistry
     });
   }
 
-  override async archive(
+  async archive(
     workspaceId: string,
     archivedAt: string,
     context?: WorkspaceArchiveContext,
-  ): Promise<void> {
-    const workspace = await super.update(workspaceId, (existing) => ({
-      ...existing,
-      updatedAt: archivedAt,
-      archivedAt,
-      ...(context?.autoArchivedChangeRequestUrl
-        ? { autoArchivedChangeRequestUrl: context.autoArchivedChangeRequestUrl }
-        : {}),
-    }));
-    if (!workspace) return;
+  ): Promise<boolean> {
+    const [workspace] = await this.mutateMany((records) => {
+      const existing = records.get(workspaceId);
+      if (!existing || existing.archivedAt) return [];
+      return [
+        {
+          ...existing,
+          updatedAt: archivedAt,
+          archivedAt,
+          ...(context?.autoArchivedChangeRequestUrl
+            ? { autoArchivedChangeRequestUrl: context.autoArchivedChangeRequestUrl }
+            : {}),
+        },
+      ];
+    });
+    if (!workspace) return false;
     await this.notifyMutation({ kind: "archive", workspaceId, workspace });
+    return true;
   }
 
   override async remove(workspaceId: string): Promise<void> {