diff --git a/assistant/src/memory/v3/__tests__/validate.test.ts b/assistant/src/memory/v3/__tests__/validate.test.ts
new file mode 100644
index 00000000000..693247e8946
--- /dev/null
+++ b/assistant/src/memory/v3/__tests__/validate.test.ts
@@ -0,0 +1,245 @@
+/**
+ * Tests for `assistant/src/memory/v3/validate.ts`.
+ *
+ * Coverage matrix — one fixture per defect category plus a clean-tree control:
+ *   - clean tree → every list empty, every count 0.
+ *   - danglingChildRefs → a `node:` ref and a `page:` ref to absent targets.
+ *   - orphanPages → a concept page on disk not wired into the tree; synthetic
+ *     page-index entries (none here) and reachable pages excluded.
+ *   - cycles → A → B → A back-edge detected during the full descent.
+ *   - staleIndex → a parent node whose mtime predates a `node:` child's mtime.
+ *   - unknownEdgeTargets → a page `edges:` entry pointing at a missing slug.
+ *
+ * Tests use temp workspaces under `os.tmpdir()`; they never touch `~/.vellum/`.
+ * mtimes are pinned with `utimes` so the freshness check is deterministic and
+ * independent of write ordering / filesystem timestamp granularity.
+ */
+
+import { mkdtempSync, rmSync } from "node:fs";
+import { utimes } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { afterEach, beforeEach, describe, expect, test } from "bun:test";
+
+import { invalidateEdgeIndex } from "../../v2/edge-index.js";
+import { invalidatePageIndex } from "../../v2/page-index.js";
+import { writePage } from "../../v2/page-store.js";
+import type { ConceptPage } from "../../v2/types.js";
+import { invalidateTreeIndex } from "../tree-index.js";
+import { getTreeDir, ROOT_NODE_ID, writeNode } from "../tree-store.js";
+import type { TreeNode } from "../types.js";
+import { validateTree } from "../validate.js";
+
+let workspaceDir: string;
+
+beforeEach(() => {
+  workspaceDir = mkdtempSync(join(tmpdir(), "vellum-tree-validate-test-"));
+});
+
+afterEach(() => {
+  invalidateTreeIndex();
+  invalidatePageIndex();
+  invalidateEdgeIndex();
+  rmSync(workspaceDir, { recursive: true, force: true });
+});
+
+function node(id: string, children: string[], body = `body ${id}`): TreeNode {
+  return { id, frontmatter: { children }, body };
+}
+
+function page(slug: string, edges: string[] = []): ConceptPage {
+  return {
+    slug,
+    frontmatter: { edges, ref_files: [], ref_urls: [] },
+    body: `body ${slug}`,
+  };
+}
+
+/** Pin a node file's mtime (and atime) to an explicit epoch-ms value. */
+async function setNodeMtime(id: string, mtimeMs: number): Promise<void> {
+  const path = join(getTreeDir(workspaceDir), `${id}.md`);
+  const t = new Date(mtimeMs);
+  await utimes(path, t, t);
+}
+
+/**
+ * Invalidate every cached index after seeding so the first `validateTree` of a
+ * test body sees the on-disk fixture rather than a stale cache.
+ */
+function resetCaches(): void {
+  invalidateTreeIndex();
+  invalidatePageIndex();
+  invalidateEdgeIndex();
+}
+
+describe("validateTree — clean tree", () => {
+  test("returns an empty report for a well-formed tree", async () => {
+    // _root → node:people → page:alice ; all refs resolve, alice reachable.
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, ["node:people"]));
+    await writeNode(workspaceDir, node("people", ["page:alice"]));
+    await writePage(workspaceDir, page("alice"));
+    // Parent newest so the freshness check never fires on a clean tree.
+    await setNodeMtime("people", 1_000);
+    await setNodeMtime(ROOT_NODE_ID, 2_000);
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.danglingChildRefs).toEqual([]);
+    expect(report.danglingChildRefCount).toBe(0);
+    expect(report.orphanPages).toEqual([]);
+    expect(report.orphanPageCount).toBe(0);
+    expect(report.cycles).toEqual([]);
+    expect(report.cycleCount).toBe(0);
+    expect(report.staleIndex).toEqual([]);
+    expect(report.staleIndexCount).toBe(0);
+    expect(report.unknownEdgeTargets).toEqual([]);
+    expect(report.unknownEdgeTargetCount).toBe(0);
+  });
+});
+
+describe("validateTree — danglingChildRefs", () => {
+  test("flags node: and page: refs whose targets are missing", async () => {
+    await writeNode(
+      workspaceDir,
+      node(ROOT_NODE_ID, ["node:ghost", "page:missing-page"]),
+    );
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.danglingChildRefs).toEqual([
+      { node: ROOT_NODE_ID, ref: "ghost", kind: "node" },
+      { node: ROOT_NODE_ID, ref: "missing-page", kind: "page" },
+    ]);
+    expect(report.danglingChildRefCount).toBe(2);
+  });
+
+  test("does not flag refs whose targets exist", async () => {
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, ["node:child"]));
+    await writeNode(workspaceDir, node("child", ["page:alice"]));
+    await writePage(workspaceDir, page("alice"));
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.danglingChildRefs).toEqual([]);
+  });
+});
+
+describe("validateTree — orphanPages", () => {
+  test("flags concept pages not reachable from the root", async () => {
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, ["page:reached"]));
+    await writePage(workspaceDir, page("reached"));
+    await writePage(workspaceDir, page("orphan"));
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.orphanPages).toEqual(["orphan"]);
+    expect(report.orphanPageCount).toBe(1);
+  });
+
+  test("a page hanging off an unreachable node is still an orphan", async () => {
+    // `floating` is not referenced by _root, so its page child is unreachable.
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, []));
+    await writeNode(workspaceDir, node("floating", ["page:detached"]));
+    await writePage(workspaceDir, page("detached"));
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.orphanPages).toEqual(["detached"]);
+  });
+});
+
+describe("validateTree — cycles", () => {
+  test("detects an A → B → A node cycle as a back-edge", async () => {
+    // _root → node:a → node:b → node:a (cycle closes on the b → a edge).
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, ["node:a"]));
+    await writeNode(workspaceDir, node("a", ["node:b"]));
+    await writeNode(workspaceDir, node("b", ["node:a"]));
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.cycles).toEqual([{ from: "b", to: "a" }]);
+    expect(report.cycleCount).toBe(1);
+  });
+
+  test("a shared DAG sub-node (two parents, no cycle) is not a cycle", async () => {
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, ["node:p1", "node:p2"]));
+    await writeNode(workspaceDir, node("p1", ["node:shared"]));
+    await writeNode(workspaceDir, node("p2", ["node:shared"]));
+    await writeNode(workspaceDir, node("shared", []));
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.cycles).toEqual([]);
+  });
+});
+
+describe("validateTree — staleIndex", () => {
+  test("flags a node whose mtime predates a node: child's mtime", async () => {
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, ["node:child"]));
+    await writeNode(workspaceDir, node("child", []));
+    // Parent older than child → stale.
+    await setNodeMtime(ROOT_NODE_ID, 1_000);
+    await setNodeMtime("child", 5_000);
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.staleIndex).toEqual([
+      {
+        node: ROOT_NODE_ID,
+        child: "child",
+        nodeMtimeMs: 1_000,
+        childMtimeMs: 5_000,
+      },
+    ]);
+    expect(report.staleIndexCount).toBe(1);
+  });
+
+  test("a parent newer than its child is not stale", async () => {
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, ["node:child"]));
+    await writeNode(workspaceDir, node("child", []));
+    await setNodeMtime("child", 1_000);
+    await setNodeMtime(ROOT_NODE_ID, 5_000);
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.staleIndex).toEqual([]);
+  });
+});
+
+describe("validateTree — unknownEdgeTargets", () => {
+  test("flags a page edge pointing at a missing slug", async () => {
+    await writeNode(workspaceDir, node(ROOT_NODE_ID, ["page:alice"]));
+    await writePage(workspaceDir, page("alice", ["nonexistent"]));
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.unknownEdgeTargets).toEqual([
+      { from: "alice", to: "nonexistent" },
+    ]);
+    expect(report.unknownEdgeTargetCount).toBe(1);
+  });
+
+  test("an edge to an existing page is not flagged", async () => {
+    await writeNode(
+      workspaceDir,
+      node(ROOT_NODE_ID, ["page:alice", "page:bob"]),
+    );
+    await writePage(workspaceDir, page("alice", ["bob"]));
+    await writePage(workspaceDir, page("bob"));
+    resetCaches();
+
+    const report = await validateTree(workspaceDir);
+
+    expect(report.unknownEdgeTargets).toEqual([]);
+  });
+});
diff --git a/assistant/src/memory/v3/tree-store.ts b/assistant/src/memory/v3/tree-store.ts
index 55dc023f2fd..86933c100ac 100644
--- a/assistant/src/memory/v3/tree-store.ts
+++ b/assistant/src/memory/v3/tree-store.ts
@@ -33,6 +33,7 @@ import {
   readFile,
   rename,
   rm,
+  stat,
   writeFile,
 } from "node:fs/promises";
 import { dirname, join, relative, sep } from "node:path";
@@ -270,6 +271,26 @@ export async function readNode(
   return { id, frontmatter, body };
 }
 
+/**
+ * File mtime for a tree node, in epoch ms. Returns 0 when the file is missing
+ * or unreadable — callers treat 0 as "no mtime" (e.g. the validator's stale-
+ * index check reads a missing node as the oldest possible mtime so it never
+ * spuriously flags a parent against an absent child). Mirrors v2's
+ * `getPageMtimeMs`.
+ */
+export async function getNodeMtimeMs(
+  workspaceDir: string,
+  id: string,
+): Promise<number> {
+  validateNodeId(id);
+  try {
+    const s = await stat(getNodePath(workspaceDir, id));
+    return s.mtimeMs;
+  } catch {
+    return 0;
+  }
+}
+
 /**
  * Write a tree node atomically (temp file + rename). A crash between the temp
  * write and the rename leaves the prior file intact; a crash after the rename
diff --git a/assistant/src/memory/v3/validate.ts b/assistant/src/memory/v3/validate.ts
new file mode 100644
index 00000000000..4a0acb2efc3
--- /dev/null
+++ b/assistant/src/memory/v3/validate.ts
@@ -0,0 +1,300 @@
+/**
+ * Memory v3 — Tree structure validator.
+ *
+ * The v3 tree is hand-authored by a data-migration during the v2 → v3 rollout
+ * (nodes reference pages and sub-nodes by `page:`/`node:` refs). Because the
+ * structure is authored, not derived, it can drift: a ref can dangle, a page
+ * can be left unwired, two nodes can reference each other into a cycle, a
+ * parent node's compositional summary can fall behind a freshly-edited child,
+ * or a page `edges:` entry can point at a slug with no page.
+ *
+ * `validateTree` is the read-only report the migration (and any later
+ * structure-health probe) runs to surface those defects. It is deliberately
+ * **non-throwing**: the migration is in progress, so an incomplete tree is
+ * expected — the report is informational, and the caller decides what (if
+ * anything) is fatal. It builds the three indices it needs (tree, page, edge),
+ * walks the DAG, and returns counts plus the offending ids for each category.
+ *
+ * Categories:
+ *   - `danglingChildRefs` — a node `children` entry (`node:`/`page:`) whose
+ *     target node/page does not exist on disk.
+ *   - `orphanPages` — concept pages present in the page index but not reachable
+ *     from the tree root by descending every `node:` child. Informational while
+ *     the migration is mid-flight (not every page is wired in yet). Synthetic
+ *     page-index entries (skills, CLI commands) are excluded — they are never
+ *     tree members.
+ *   - `cycles` — back-edges found during a full DFS over `node:` adjacency
+ *     (A → B → A). A cycle would make a naive descent loop forever.
+ *   - `staleIndex` — a node whose own file mtime predates one of its `node:`
+ *     children's mtime, hinting its compositional index/summary may be out of
+ *     date relative to the child it composes.
+ *   - `unknownEdgeTargets` — page `edges:` targets with no corresponding page
+ *     index slug, reusing v2's `validateEdgeTargets`.
+ */
+
+import { CLI_COMMAND_SLUG_PREFIX } from "../v2/cli-command-store.js";
+import { getEdgeIndex, validateEdgeTargets } from "../v2/edge-index.js";
+import { getPageIndex } from "../v2/page-index.js";
+import { SKILL_SLUG_PREFIX } from "../v2/skill-store.js";
+import { getTreeIndex, type TreeIndex } from "./tree-index.js";
+import { getNodeMtimeMs } from "./tree-store.js";
+
+/**
+ * A `node:` child whose mtime is newer than the parent node that composes it.
+ * `node` is the parent, `child` the fresher child, and the two `*MtimeMs`
+ * fields are their epoch-ms mtimes (parent < child triggers the report).
+ */
+export interface StaleIndexEntry {
+  node: string;
+  child: string;
+  nodeMtimeMs: number;
+  childMtimeMs: number;
+}
+
+/**
+ * Read-only health report over the v3 tree + its referenced pages/edges.
+ * Every list is sorted for deterministic output; `*Count` fields mirror the
+ * corresponding list length so callers can summarize without re-counting.
+ */
+export interface TreeValidationReport {
+  /** `node:`/`page:` children whose target does not exist. */
+  danglingChildRefs: Array<{
+    node: string;
+    ref: string;
+    kind: "node" | "page";
+  }>;
+  danglingChildRefCount: number;
+  /** Concept pages not reachable from the root by descending all node children. */
+  orphanPages: string[];
+  orphanPageCount: number;
+  /** Back-edges (`from → to`) closing a cycle during the full DFS descent. */
+  cycles: Array<{ from: string; to: string }>;
+  cycleCount: number;
+  /** Nodes whose mtime predates a child node's mtime. */
+  staleIndex: StaleIndexEntry[];
+  staleIndexCount: number;
+  /** Page `edges:` targets with no corresponding page-index slug. */
+  unknownEdgeTargets: Array<{ from: string; to: string }>;
+  unknownEdgeTargetCount: number;
+}
+
+/** True when a page-index slug is a synthetic (non-concept-page) entry. */
+function isSyntheticSlug(slug: string): boolean {
+  return (
+    slug.startsWith(SKILL_SLUG_PREFIX) ||
+    slug.startsWith(CLI_COMMAND_SLUG_PREFIX)
+  );
+}
+
+/**
+ * Collect dangling `node:`/`page:` child refs: every node child whose target
+ * node id is absent from `tree.nodes`, and every page child whose slug is
+ * absent from `knownPageSlugs`. Sorted by `(node, kind, ref)`.
+ */
+function collectDanglingChildRefs(
+  tree: TreeIndex,
+  knownPageSlugs: ReadonlySet<string>,
+): Array<{ node: string; ref: string; kind: "node" | "page" }> {
+  const dangling: Array<{ node: string; ref: string; kind: "node" | "page" }> =
+    [];
+  for (const [nodeId, children] of tree.childrenByNode) {
+    for (const child of children) {
+      const exists =
+        child.kind === "node"
+          ? tree.nodes.has(child.ref)
+          : knownPageSlugs.has(child.ref);
+      if (!exists) {
+        dangling.push({ node: nodeId, ref: child.ref, kind: child.kind });
+      }
+    }
+  }
+  dangling.sort(
+    (a, b) =>
+      a.node.localeCompare(b.node) ||
+      a.kind.localeCompare(b.kind) ||
+      a.ref.localeCompare(b.ref),
+  );
+  return dangling;
+}
+
+/**
+ * Resolve the existing `node:` children of `nodeId`, in `children` order. Refs
+ * to absent nodes are skipped (those are reported separately as dangling) so
+ * the descent never recurses into a node that isn't on disk.
+ */
+function nodeChildrenOf(tree: TreeIndex, nodeId: string): string[] {
+  const children = tree.childrenByNode.get(nodeId) ?? [];
+  const out: string[] = [];
+  for (const child of children) {
+    if (child.kind === "node" && tree.nodes.has(child.ref)) {
+      out.push(child.ref);
+    }
+  }
+  return out;
+}
+
+/**
+ * Full DFS over `node:` adjacency from `tree.root`. Returns the set of
+ * reachable node ids (for orphan-page reachability) and the back-edges that
+ * close a cycle. A back-edge is an edge into a node still on the active
+ * recursion stack (classic gray-node cycle detection); `visited` (black)
+ * prevents re-walking shared DAG sub-nodes.
+ */
+function descend(tree: TreeIndex): {
+  reachableNodes: Set<string>;
+  cycles: Array<{ from: string; to: string }>;
+} {
+  const reachableNodes = new Set<string>();
+  const onStack = new Set<string>();
+  const cycles: Array<{ from: string; to: string }> = [];
+
+  // Iterative DFS with an explicit stack so deep trees don't blow the call
+  // stack. Each frame tracks its child cursor; we push a child frame, and on
+  // exhaustion pop the parent off the recursion stack (`onStack`).
+  type Frame = { node: string; children: string[]; cursor: number };
+  const stack: Frame[] = [];
+
+  function enter(nodeId: string): void {
+    reachableNodes.add(nodeId);
+    onStack.add(nodeId);
+    stack.push({
+      node: nodeId,
+      children: nodeChildrenOf(tree, nodeId),
+      cursor: 0,
+    });
+  }
+
+  if (tree.nodes.has(tree.root)) {
+    enter(tree.root);
+  }
+
+  while (stack.length > 0) {
+    const frame = stack[stack.length - 1];
+    if (frame.cursor >= frame.children.length) {
+      onStack.delete(frame.node);
+      stack.pop();
+      continue;
+    }
+    const child = frame.children[frame.cursor++];
+    if (onStack.has(child)) {
+      // Edge into an ancestor still on the stack → cycle-closing back-edge.
+      cycles.push({ from: frame.node, to: child });
+      continue;
+    }
+    if (reachableNodes.has(child)) {
+      // Already fully explored via another parent (shared DAG sub-node).
+      continue;
+    }
+    enter(child);
+  }
+
+  cycles.sort(
+    (a, b) => a.from.localeCompare(b.from) || a.to.localeCompare(b.to),
+  );
+  return { reachableNodes, cycles };
+}
+
+/**
+ * Concept pages reachable from the tree: every `page:` child of a reachable
+ * node. Pages hanging off unreachable nodes are *not* counted reachable — they
+ * only become reachable once their parent chain links back to the root.
+ */
+function reachablePages(
+  tree: TreeIndex,
+  reachableNodes: ReadonlySet<string>,
+): Set<string> {
+  const pages = new Set<string>();
+  for (const nodeId of reachableNodes) {
+    for (const child of tree.childrenByNode.get(nodeId) ?? []) {
+      if (child.kind === "page") pages.add(child.ref);
+    }
+  }
+  return pages;
+}
+
+/**
+ * Nodes whose own mtime predates one of their `node:` children's mtime. A
+ * missing node file reads as mtime 0 (oldest), so the check never flags a
+ * parent against an absent child. Sorted by `(node, child)`.
+ */
+async function collectStaleIndex(
+  workspaceDir: string,
+  tree: TreeIndex,
+): Promise<StaleIndexEntry[]> {
+  const ids = [...tree.nodes.keys()];
+  const mtimes = new Map<string, number>();
+  await Promise.all(
+    ids.map(async (id) => {
+      mtimes.set(id, await getNodeMtimeMs(workspaceDir, id));
+    }),
+  );
+
+  const stale: StaleIndexEntry[] = [];
+  for (const node of ids) {
+    const nodeMtimeMs = mtimes.get(node) ?? 0;
+    for (const child of nodeChildrenOf(tree, node)) {
+      const childMtimeMs = mtimes.get(child) ?? 0;
+      if (nodeMtimeMs < childMtimeMs) {
+        stale.push({ node, child, nodeMtimeMs, childMtimeMs });
+      }
+    }
+  }
+  stale.sort(
+    (a, b) => a.node.localeCompare(b.node) || a.child.localeCompare(b.child),
+  );
+  return stale;
+}
+
+/**
+ * Validate the hand-authored v3 tree structure for `workspaceDir` and return a
+ * {@link TreeValidationReport}. Builds the tree, page, and edge indices, walks
+ * the DAG from the root, and reports the five defect categories. Never throws —
+ * it is a report, not an assertion.
+ */
+export async function validateTree(
+  workspaceDir: string,
+): Promise<TreeValidationReport> {
+  const [tree, pageIndex, edgeIndex] = await Promise.all([
+    getTreeIndex(workspaceDir),
+    getPageIndex(workspaceDir),
+    getEdgeIndex(workspaceDir),
+  ]);
+
+  const knownPageSlugs = new Set(pageIndex.bySlug.keys());
+
+  // Kick off the stale-index mtime stats up front — it only depends on the
+  // tree, not on the DAG walk below — so its filesystem reads overlap the
+  // (synchronous) descent rather than running strictly after it.
+  const staleIndexPromise = collectStaleIndex(workspaceDir, tree);
+
+  const danglingChildRefs = collectDanglingChildRefs(tree, knownPageSlugs);
+
+  const { reachableNodes, cycles } = descend(tree);
+
+  const reached = reachablePages(tree, reachableNodes);
+  const orphanPages = [...knownPageSlugs]
+    .filter((slug) => !isSyntheticSlug(slug) && !reached.has(slug))
+    .sort();
+
+  const staleIndex = await staleIndexPromise;
+
+  // Edge graph is page-only; knownSlugs is the full page-index slug set so an
+  // edge pointing at a skill/CLI entry is not spuriously flagged unknown.
+  const unknownEdgeTargets = validateEdgeTargets(
+    edgeIndex,
+    knownPageSlugs,
+  ).missing;
+
+  return {
+    danglingChildRefs,
+    danglingChildRefCount: danglingChildRefs.length,
+    orphanPages,
+    orphanPageCount: orphanPages.length,
+    cycles,
+    cycleCount: cycles.length,
+    staleIndex,
+    staleIndexCount: staleIndex.length,
+    unknownEdgeTargets,
+    unknownEdgeTargetCount: unknownEdgeTargets.length,
+  };
+}