diff --git a/docs/TASKS.md b/docs/TASKS.md
index b8c4fb0..e9dda35 100644
--- a/docs/TASKS.md
+++ b/docs/TASKS.md
@@ -54,3 +54,7 @@ Active workstream is **W1 — Federation v1**. Workers should:
 ## P6 — Docs, compliance matrix, alpha tag (#606) — feat/p6-docs-compliance-alpha
 
 - Status: in-repo deliverables done (CONTRIBUTING.md + harness×gate compliance matrix + check-resident-budget.sh + CI wiring + ALPHA-DOD.md). Remaining: alpha tag v0.0.39-alpha (Lead, post-merge). aiguide reconcile merged (#8). Detail: scratchpads/p6-docs-compliance-alpha.md.
+
+## F3-m3 — mosaic update re-seeds framework + relaunches agents (#609) — feat/f3-m3-update-reseed
+
+- Status: implemented + tested. Closes R13: `mosaic update` now re-seeds the framework (data-safe MOSAIC_SYNC_ONLY) after the CLI install so shipped launcher/runtime changes activate; `--relaunch` restarts rostered agents; `--no-reseed` opts out. Detail: scratchpads/f3-m3-update-reseed.md.
diff --git a/docs/scratchpads/f3-m3-update-reseed.md b/docs/scratchpads/f3-m3-update-reseed.md
new file mode 100644
index 0000000..afa9dfa
--- /dev/null
+++ b/docs/scratchpads/f3-m3-update-reseed.md
@@ -0,0 +1,29 @@
+# F3-m3 — `mosaic update` re-seeds framework + relaunches agents (R13)
+
+- **Issue:** #609 · **Branch:** `feat/f3-m3-update-reseed`
+
+## Gap (found in 0.0.39 production validation)
+
+`mosaic update` installs the new npm CLI but never re-seeds `~/.config/mosaic/` from the package's
+bundled `framework/`. So the shipped custom Pi harness (agent-name export + native HB, 0.0.39) stays
+DORMANT until a re-seed — operators get the new CLI on a stale framework.
+
+## Implementation
+
+- `update-checker.ts`: `resolveBundledFrameworkRoot()`, `buildReseedCommand()` (install.sh in
+  `MOSAIC_SYNC_ONLY=1 MOSAIC_INSTALL_MODE=keep` — the P4 data-safe reconcile), `runFrameworkReseed()`,
+  `readRosterAgentNames()`, `buildRelaunchCommands()` (systemctl --user restart per agent).
+- `cli.ts` `update`: after a successful CLI install that includes `@mosaicstack/mosaic`, re-seed the
+  framework (default-on; `--no-reseed` to skip). Then either `--relaunch` (restart rostered agents) or
+  print clear guidance to run `mosaic update --relaunch` / `mosaic fleet restart`.
+
+## Flow
+
+`update CLI → re-seed framework (data-safe) → relaunch agents (opt-in)` — closes R13, activates the
+native harness for every operator.
+
+## Verification
+
+- 6 new unit tests (reseed command/env, relaunch commands, roster parse, missing-installer guard).
+- 19 runtime + 26 launch tests still green; tsc/eslint/prettier clean.
+- Data-safety of the sync is already proven (P4 5-fixture matrix + live dragon-lin validation).
diff --git a/packages/mosaic/src/cli.ts b/packages/mosaic/src/cli.ts
index ab955d9..187bbbd 100644
--- a/packages/mosaic/src/cli.ts
+++ b/packages/mosaic/src/cli.ts
@@ -26,6 +26,10 @@ import {
   checkForAllUpdates,
   formatAllPackagesTable,
   getInstallAllCommand,
+  runFrameworkReseed,
+  readRosterAgentNames,
+  buildRelaunchCommands,
+  FRAMEWORK_RESEED_PACKAGE,
 } from './runtime/update-checker.js';
 import { runWizard } from './wizard.js';
 import { ClackPrompter } from './prompter/clack-prompter.js';
@@ -404,7 +408,12 @@ program
   .command('update')
   .description('Check for and install Mosaic CLI updates')
   .option('--check', 'Check only, do not install')
-  .action(async (opts: { check?: boolean }) => {
+  .option(
+    '--no-reseed',
+    'Skip re-seeding framework files into ~/.config/mosaic after the CLI update',
+  )
+  .option('--relaunch', 'Restart durable fleet agents so the new launcher/runtime takes effect')
+  .action(async (opts: { check?: boolean; reseed?: boolean; relaunch?: boolean }) => {
     // checkForAllUpdates imported statically above
     const { execSync } = await import('node:child_process');
 
@@ -442,6 +451,51 @@ program
       console.error('\nUpdate failed. Try manually: bash tools/install.sh');
       process.exit(1);
     }
+
+    // F3-m3 / R13: the CLI is updated, but the framework files in
+    // ~/.config/mosaic/ are still the previous version. Re-seed them from the
+    // freshly-installed package so shipped launcher/runtime changes ACTIVATE.
+    // Only when the framework-bearing package itself updated.
+    const mosaicUpdated = outdated.some(
+      (r: { package: string }) => r.package === FRAMEWORK_RESEED_PACKAGE,
+    );
+    if (mosaicUpdated && opts.reseed !== false) {
+      console.log(
+        '\nRe-seeding framework files into ~/.config/mosaic (data-safe; keeps your edits)…',
+      );
+      const reseed = runFrameworkReseed();
+      if (reseed.ok) {
+        console.log('✔ Framework re-seeded.');
+        const agents = readRosterAgentNames();
+        if (agents.length > 0) {
+          if (opts.relaunch) {
+            console.log(
+              `\nRelaunching ${agents.length} fleet agent(s) to pick up the new runtime…`,
+            );
+            for (const restart of buildRelaunchCommands(agents)) {
+              try {
+                execSync(restart.join(' '), { stdio: 'inherit', timeout: 30_000 });
+              } catch {
+                console.error(`  ⚠ failed to restart agent — run: ${restart.join(' ')}`);
+              }
+            }
+            console.log('✔ Agents relaunched.');
+          } else {
+            console.log(
+              `\nℹ ${agents.length} fleet agent(s) are still running the previous runtime. ` +
+                'Restart them to activate the update:\n    mosaic update --relaunch   ' +
+                '(or: mosaic fleet restart <agent>)',
+            );
+          }
+        }
+      } else {
+        console.error(
+          `\n⚠ Framework re-seed skipped: ${reseed.reason ?? 'unknown'}.\n` +
+            '  Activate manually: bash "$(npm root -g)/@mosaicstack/mosaic/framework/install.sh" ' +
+            '(MOSAIC_SYNC_ONLY=1 MOSAIC_INSTALL_MODE=keep)',
+        );
+      }
+    }
   });
 
 // ─── wizard ─────────────────────────────────────────────────────────────
diff --git a/packages/mosaic/src/runtime/update-checker.reseed.spec.ts b/packages/mosaic/src/runtime/update-checker.reseed.spec.ts
new file mode 100644
index 0000000..932cdd4
--- /dev/null
+++ b/packages/mosaic/src/runtime/update-checker.reseed.spec.ts
@@ -0,0 +1,85 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtempSync, mkdirSync, writeFileSync, rmSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import {
+  buildReseedCommand,
+  buildRelaunchCommands,
+  readRosterAgentNames,
+  runFrameworkReseed,
+} from './update-checker.js';
+
+/**
+ * F3-m3 / R13: `mosaic update` re-seeds the framework + (opt-in) relaunches
+ * durable agents so shipped launcher/runtime changes activate. These cover the
+ * pure builders + the missing-installer guard (the exec path is integration).
+ */
+
+describe('buildReseedCommand', () => {
+  it('invokes the package install.sh in data-safe sync-only keep mode', () => {
+    const out = buildReseedCommand('/pkg/framework', '/home/u/.config/mosaic');
+    expect(out.installer).toBe('/pkg/framework/install.sh');
+    expect(out.command).toBe('bash /pkg/framework/install.sh');
+    expect(out.env).toEqual({
+      MOSAIC_SYNC_ONLY: '1',
+      MOSAIC_INSTALL_MODE: 'keep',
+      MOSAIC_HOME: '/home/u/.config/mosaic',
+    });
+  });
+});
+
+describe('buildRelaunchCommands', () => {
+  it('builds a systemctl --user restart per agent unit', () => {
+    expect(buildRelaunchCommands(['orchestrator', 'coder0'])).toEqual([
+      ['systemctl', '--user', 'restart', 'mosaic-agent@orchestrator.service'],
+      ['systemctl', '--user', 'restart', 'mosaic-agent@coder0.service'],
+    ]);
+  });
+
+  it('is empty for an empty roster', () => {
+    expect(buildRelaunchCommands([])).toEqual([]);
+  });
+});
+
+describe('readRosterAgentNames', () => {
+  let home: string;
+
+  beforeEach(() => {
+    home = mkdtempSync(join(tmpdir(), 'mosaic-roster-'));
+  });
+  afterEach(() => {
+    rmSync(home, { recursive: true, force: true });
+  });
+
+  it('returns [] when no roster exists', () => {
+    expect(readRosterAgentNames(home)).toEqual([]);
+  });
+
+  it('extracts agent names from roster.yaml', () => {
+    mkdirSync(join(home, 'fleet'), { recursive: true });
+    writeFileSync(
+      join(home, 'fleet', 'roster.yaml'),
+      [
+        'version: 1',
+        'agents:',
+        '  - name: orchestrator',
+        '    runtime: pi',
+        '  - name: coder0',
+        '    runtime: claude',
+        '  - name: "reviewer-1"',
+        '    runtime: codex',
+      ].join('\n') + '\n',
+    );
+    expect(readRosterAgentNames(home)).toEqual(['orchestrator', 'coder0', 'reviewer-1']);
+  });
+});
+
+describe('runFrameworkReseed', () => {
+  it('reports not-ok (not throw) when the installer is absent', () => {
+    const missing = mkdtempSync(join(tmpdir(), 'mosaic-noinstaller-'));
+    const res = runFrameworkReseed(missing, join(missing, 'home'));
+    expect(res.ok).toBe(false);
+    expect(res.reason).toContain('installer not found');
+    rmSync(missing, { recursive: true, force: true });
+  });
+});
diff --git a/packages/mosaic/src/runtime/update-checker.ts b/packages/mosaic/src/runtime/update-checker.ts
index 855a067..d56836e 100644
--- a/packages/mosaic/src/runtime/update-checker.ts
+++ b/packages/mosaic/src/runtime/update-checker.ts
@@ -16,7 +16,8 @@
 import { execSync } from 'node:child_process';
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs';
 import { homedir } from 'node:os';
-import { join } from 'node:path';
+import { dirname, join, resolve } from 'node:path';
+import { fileURLToPath } from 'node:url';
 
 // ─── Types ──────────────────────────────────────────────────────────────────
 
@@ -453,6 +454,98 @@ export function getInstallAllCommand(outdated: PackageUpdateResult[]): string {
   return `npm i -g ${pkgs.join(' ')}`;
 }
 
+// ─── Post-update framework re-seed + agent relaunch (F3-m3 / R13) ─────────────
+//
+// `mosaic update` installs the new npm CLI but, on its own, leaves the framework
+// files in ~/.config/mosaic/ stale — so shipped launcher/runtime changes (e.g.
+// the agent-name export + native heartbeat) never ACTIVATE until a re-seed.
+// These helpers run the package's own install.sh in sync-only mode (the P4
+// data-safe reconcile: framework-owned overwrite + backup-once; SOUL/USER/
+// *.local/credentials preserved) and, opt-in, relaunch durable agents.
+
+/** Resolve the framework/ directory bundled in the installed package. */
+export function resolveBundledFrameworkRoot(): string {
+  // dist/runtime/update-checker.js → ../../framework (package files: dist + framework)
+  return resolve(dirname(fileURLToPath(import.meta.url)), '..', '..', 'framework');
+}
+
+export const FRAMEWORK_RESEED_PACKAGE = PKG;
+
+/**
+ * Build the framework re-seed invocation: the package's install.sh in
+ * sync-only mode (file phase only — no environment-touching post-install),
+ * keep mode (never overwrite user files). Returned as data so it is unit
+ * testable; `runFrameworkReseed` executes it.
+ */
+export function buildReseedCommand(
+  frameworkRoot: string,
+  mosaicHome: string,
+): { installer: string; command: string; env: Record<string, string> } {
+  const installer = join(frameworkRoot, 'install.sh');
+  return {
+    installer,
+    command: `bash ${installer}`,
+    env: {
+      MOSAIC_SYNC_ONLY: '1',
+      MOSAIC_INSTALL_MODE: 'keep',
+      MOSAIC_HOME: mosaicHome,
+    },
+  };
+}
+
+/**
+ * Re-seed the framework from the freshly-installed package. Returns a result
+ * describing what happened (so callers can message + decide on relaunch).
+ * Best-effort: a missing installer or a non-zero exit is reported, not thrown.
+ */
+export function runFrameworkReseed(
+  frameworkRoot = resolveBundledFrameworkRoot(),
+  mosaicHome = join(homedir(), '.config', 'mosaic'),
+): { ok: boolean; reason?: string } {
+  const { installer, command, env } = buildReseedCommand(frameworkRoot, mosaicHome);
+  if (!existsSync(installer)) {
+    return { ok: false, reason: `installer not found: ${installer}` };
+  }
+  try {
+    execSync(command, { stdio: 'inherit', env: { ...process.env, ...env }, timeout: 120_000 });
+    return { ok: true };
+  } catch (err) {
+    return { ok: false, reason: err instanceof Error ? err.message : String(err) };
+  }
+}
+
+/**
+ * Best-effort parse of the fleet roster for agent names (used to relaunch
+ * durable agents after a re-seed). Returns [] when no roster exists.
+ */
+export function readRosterAgentNames(mosaicHome = join(homedir(), '.config', 'mosaic')): string[] {
+  const rosterPath = join(mosaicHome, 'fleet', 'roster.yaml');
+  if (!existsSync(rosterPath)) return [];
+  let text: string;
+  try {
+    text = readFileSync(rosterPath, 'utf-8');
+  } catch {
+    return [];
+  }
+  // Roster agents are listed as `- name: <id>` entries under `agents:`.
+  const names: string[] = [];
+  for (const line of text.split('\n')) {
+    const m = line.match(/^\s*-?\s*name:\s*["']?([A-Za-z0-9._-]+)["']?\s*$/);
+    if (m && m[1]) names.push(m[1]);
+  }
+  return names;
+}
+
+/** Build the per-agent systemd relaunch commands (drain+relaunch via restart). */
+export function buildRelaunchCommands(agentNames: string[]): string[][] {
+  return agentNames.map((name) => [
+    'systemctl',
+    '--user',
+    'restart',
+    `mosaic-agent@${name}.service`,
+  ]);
+}
+
 /**
  * Format a table showing all packages with their current/latest versions.
  */