diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 36d4425157..7d489205bb 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -76,6 +76,15 @@ the same configuration. Pre-commit formats and lints staged files; pre-push runs
 `check:fast`.
 `docs:check` checks committed generated metadata. `docs:generate` regenerates
 those files, and the docs CI lane checks them.
+The committed product catalog contains documented facts and their provider
+identity, rather than full runtime schema hashes. The managed skill contains
+instructions and inventory metadata; doctor compares its installed files with
+the canonical bundle. Schema-only fixes should not change these files or the
+skill commitment in the conformance manifest. Runtime schema identity remains
+available through doctor and `binary_session`. If a branch conflicts only in
+these generated files, merge the source changes first, then run
+`npm run docs:generate` to regenerate from the merged sources; keep hand-written
+skill instructions from both branches.
 Real-provider execution remains uncached; deterministic builds use Turbo.
 
 Local `npm test` runs every deterministic Vitest project without coverage or
diff --git a/docs/product-catalog.json b/docs/product-catalog.json
index 7a83ccb5fa..3f05b7e2b0 100644
--- a/docs/product-catalog.json
+++ b/docs/product-catalog.json
@@ -713,9 +713,6 @@
       "mcp_prompts": 6
     },
     "digests": {
-      "tools_sha256": "0ac2316e6bd007d273c60f69e132341fc06a3dcb6879408ecfdd3271f30a8230",
-      "prompts_sha256": "ef2de8814390b340623c32001610aa2709d90bed51537b6e562ab3abf144ab4d",
-      "combined_sha256": "20cc1432b29f11c20206cbaeacafab927dcfd68c81a82cf198ad058f54f06eac",
       "providers_sha256": "954b499c76514890062d2b6c936d73cb3a9c45412d522a081125a325e81cdec5"
     }
   }
diff --git a/docs/verification/managed-conformance-manifest.json b/docs/verification/managed-conformance-manifest.json
index e5c28005c4..f83f01995f 100644
--- a/docs/verification/managed-conformance-manifest.json
+++ b/docs/verification/managed-conformance-manifest.json
@@ -1,5 +1,5 @@
 {
-  "manifest_id": "ecm_bee7251323bddbe561003a45ddee6c43eb9e37839983dc89e438dca6d9e5fdec",
+  "manifest_id": "ecm_0abe486e63d1ebdeec6487dfd19a5bd92d47a90d84e60df96926fa66602552ea",
   "verifier": {
     "id": "rea-managed-conformance",
     "version": "1"
@@ -13,7 +13,7 @@
   "skill_digests": [
     {
       "skill_id": "reverse-engineer-anything",
-      "sha256": "62f197bbd05ca97ff21cc69f45ccf776c152004f3c7f1bd589dfea0b8202db57"
+      "sha256": "0e6130b292e3cd3fe1da214b2b3ca5eba8661c81a5bf64679b7ef29828393f29"
     }
   ],
   "claims": [
diff --git a/scripts/generate-skill-metadata.mjs b/scripts/generate-skill-metadata.mjs
index 3d4bc4bbca..f1bdbd769c 100644
--- a/scripts/generate-skill-metadata.mjs
+++ b/scripts/generate-skill-metadata.mjs
@@ -19,13 +19,12 @@ const withCount = current.replace(
   /^\s{2}tool_count:\s*\d+\s*$/mu,
   `  tool_count: ${String(CATALOG_IDENTITY.counts.mcp_tools)}`,
 );
-const digestLine = `  catalog_digest: "${CATALOG_IDENTITY.digests.combined_sha256}"`;
-const source = /^\s{2}catalog_digest:/mu.test(withCount)
-  ? withCount.replace(
-      /^\s{2}catalog_digest:\s*"[a-f0-9]{64}"\s*$/mu,
-      digestLine,
-    )
-  : withCount.replace(/^(\s{2}tool_count:\s*\d+\s*)$/mu, `$1\n${digestLine}`);
+// Skill identity follows the installed instruction bundle. Runtime schema identity
+// is still reported independently by doctor and binary_session.
+const source = withCount.replace(
+  /^ {2}catalog_digest:[^\r\n]*(?:\r?\n|$)/mu,
+  "",
+);
 
 await ensureGeneratedFile({
   path,
diff --git a/scripts/lib/product-catalog.mjs b/scripts/lib/product-catalog.mjs
index 8c4aaae4f9..21a421b250 100644
--- a/scripts/lib/product-catalog.mjs
+++ b/scripts/lib/product-catalog.mjs
@@ -58,7 +58,7 @@ export const createProductCatalog = async (root) => {
     runtime_catalog: {
       counts: sources.catalogIdentity.CATALOG_IDENTITY.counts,
       digests: {
-        ...sources.catalogIdentity.CATALOG_IDENTITY.digests,
+        // Full runtime schema digests belong to server identity, not this facts projection.
         providers_sha256: providerCatalogDigest(providers),
       },
     },
diff --git a/skills/reverse-engineer-anything/SKILL.md b/skills/reverse-engineer-anything/SKILL.md
index f97a188a1d..79923da1f3 100644
--- a/skills/reverse-engineer-anything/SKILL.md
+++ b/skills/reverse-engineer-anything/SKILL.md
@@ -4,7 +4,6 @@ description: Reverse engineer native, managed, Electron/JavaScript, packaged, fi
 metadata:
   version: "33"
   tool_count: 139
-  catalog_digest: "20cc1432b29f11c20206cbaeacafab927dcfd68c81a82cf198ad058f54f06eac"
 ---
 
 # REA
diff --git a/src/application/Doctor.fixture.ts b/src/application/Doctor.fixture.ts
index 2c4725dfac..9f271ed221 100644
--- a/src/application/Doctor.fixture.ts
+++ b/src/application/Doctor.fixture.ts
@@ -26,7 +26,8 @@ export const createDoctorHostFixture = (
     Promise.resolve({
       version: PRODUCT_IDENTITY.skillVersion,
       toolCount: CATALOG_IDENTITY.counts.mcp_tools,
-      catalogDigest: CATALOG_IDENTITY.digests.combined_sha256,
+      catalogDigest: null,
+      canonical: true,
     }),
   ...overrides,
 });
diff --git a/src/application/Doctor.test.ts b/src/application/Doctor.test.ts
index af7881c5bf..d6845245a1 100644
--- a/src/application/Doctor.test.ts
+++ b/src/application/Doctor.test.ts
@@ -177,6 +177,7 @@ describe("doctor installation identity", () => {
             version: "10",
             toolCount: null,
             catalogDigest: null,
+            canonical: false,
           }),
       }),
     );
diff --git a/src/application/Doctor.ts b/src/application/Doctor.ts
index a4cf57e9cc..078db0d73d 100644
--- a/src/application/Doctor.ts
+++ b/src/application/Doctor.ts
@@ -14,6 +14,7 @@ import {
   readLinuxDistribution,
   type LinuxDistribution,
 } from "./LinuxHopper.js";
+import { canonicalSkillNeedsInstall } from "./SetupSkill.js";
 import { CATALOG_IDENTITY } from "../catalogIdentity.js";
 import { PRODUCT_IDENTITY, SDK_IDENTITY } from "../identity.js";
 import {
@@ -95,11 +96,13 @@ export interface DoctorHost {
   ilspyCmdVersion?(path: string): Promise<string | undefined>;
 }
 
-/** Parsed identity committed by an installed REA skill. */
+/** Observed skill metadata and comparison with the packaged instruction bundle. */
 interface InstalledSkillIdentity {
   readonly version: string | null;
   readonly toolCount: number | null;
   readonly catalogDigest: string | null;
+  /** Whether all managed instruction and reference files match this package. */
+  readonly canonical: boolean;
 }
 
 /** Structured result returned by the read-only doctor workflow. */
@@ -139,6 +142,7 @@ interface DoctorIdentity {
   readonly skill: {
     readonly installed_version: string | null;
     readonly installed_tool_count: number | null;
+    /** Legacy catalog digest observed in older bundles; current bundles omit it. */
     readonly installed_catalog_digest: string | null;
     readonly state: "aligned" | "stale" | "missing";
     readonly remediation: string | null;
@@ -253,7 +257,7 @@ const skillIdentityAligned = (
 ): boolean =>
   identity?.version === PRODUCT_IDENTITY.skillVersion &&
   identity.toolCount === CATALOG_IDENTITY.counts.mcp_tools &&
-  identity.catalogDigest === CATALOG_IDENTITY.digests.combined_sha256;
+  identity.canonical;
 
 const skillIdentityCheck = (
   identity: InstalledSkillIdentity | undefined,
@@ -507,6 +511,7 @@ const installedSkillIdentity = async (
     const content = await readInstalledSkill(home);
     const countText = /^\s{2}tool_count:\s*(\d+)\s*$/mu.exec(content)?.[1];
     return {
+      canonical: !(await canonicalSkillNeedsInstall(home)),
       version: /^\s{2}version:\s*"([^"]+)"\s*$/mu.exec(content)?.[1] ?? null,
       toolCount:
         countText === undefined ? null : Number.parseInt(countText, 10),
diff --git a/tests/boundary/cli/productCatalog.test.ts b/tests/boundary/cli/productCatalog.test.ts
index 3eb9f6528e..77fdec7df3 100644
--- a/tests/boundary/cli/productCatalog.test.ts
+++ b/tests/boundary/cli/productCatalog.test.ts
@@ -195,6 +195,11 @@ describe("canonical product catalog", () => {
       "project_managed_application_graph",
       "verify_managed_native_boundaries",
     ]);
+    // Runtime schema commitments must not fan out into checked-in documentation.
+    // Provider commitments cover the facts actually present in this projection.
+    expect(Object.keys(catalog.runtime_catalog.digests)).toEqual([
+      "providers_sha256",
+    ]);
     expect(catalog.runtime_catalog.digests.providers_sha256).toBe(
       providerCatalogDigest(catalog.providers),
     );
diff --git a/tests/boundary/filesystem/setupSkill.test.ts b/tests/boundary/filesystem/setupSkill.test.ts
index a0f0b47383..aa457b0571 100644
--- a/tests/boundary/filesystem/setupSkill.test.ts
+++ b/tests/boundary/filesystem/setupSkill.test.ts
@@ -1,4 +1,4 @@
-import { mkdir, readFile, writeFile } from "node:fs/promises";
+import { mkdir, readFile, rm, writeFile } from "node:fs/promises";
 import { dirname, join } from "node:path";
 import { describe, expect, it } from "vitest";
 import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
@@ -7,6 +7,11 @@ import {
   canonicalSkillNeedsInstall,
   installCanonicalSkill,
 } from "../../../src/application/SetupSkill.js";
+import {
+  runDoctor,
+  systemDoctorHost,
+} from "../../../src/application/Doctor.js";
+import { createDoctorHostFixture } from "../../../src/application/Doctor.fixture.js";
 import { TOOL_CONTRACTS } from "../../../src/contracts/toolContracts.js";
 import { PRODUCT_IDENTITY } from "../../../src/identity.js";
 import { skillReferenceIssues } from "../../../scripts/lib/docs-facts.mjs";
@@ -98,3 +103,62 @@ describe("canonical skill transaction", () => {
     expect(await skillReferenceIssues(dirname(destination))).toEqual([]);
   });
 });
+
+it("doctor verifies installed instructions and references even when metadata is current", async () => {
+  const home = await createTestTempDirectory("rea-skill-doctor-");
+  const destination = join(
+    home,
+    ".agents/skills/reverse-engineer-anything/SKILL.md",
+  );
+  const reference = join(
+    dirname(destination),
+    "references/evidence-workflows.md",
+  );
+  const system = systemDoctorHost({
+    environment: { HOME: home, USERPROFILE: home },
+  });
+  const host = createDoctorHostFixture({
+    installedSkillIdentity: () =>
+      system.installedSkillIdentity?.() ?? Promise.resolve(undefined),
+  });
+  expect((await runDoctor(undefined, host)).identity?.skill.state).toBe(
+    "missing",
+  );
+  expect(await installCanonicalSkill(home)).toBe("installed");
+  expect((await runDoctor(undefined, host)).identity?.skill).toMatchObject({
+    state: "aligned",
+    installed_catalog_digest: null,
+  });
+  const legacyDigest = "0".repeat(64);
+  await writeFile(
+    destination,
+    (await readFile(destination, "utf8")).replace(
+      `  tool_count: ${String(TOOL_CONTRACTS.length)}`,
+      `  tool_count: ${String(TOOL_CONTRACTS.length)}\n  catalog_digest: "${legacyDigest}"`,
+    ),
+  );
+  expect((await runDoctor(undefined, host)).identity?.skill).toMatchObject({
+    state: "stale",
+    installed_catalog_digest: legacyDigest,
+  });
+  expect(await installCanonicalSkill(home)).toBe("installed");
+  for (const path of [destination, reference]) {
+    const canonical = await readFile(path, "utf8");
+    await writeFile(path, `${canonical}\nLocally changed instructions.\n`);
+    expect((await runDoctor(undefined, host)).identity?.skill.state).toBe(
+      "stale",
+    );
+    expect(await installCanonicalSkill(home)).toBe("installed");
+    expect((await runDoctor(undefined, host)).identity?.skill.state).toBe(
+      "aligned",
+    );
+  }
+  await rm(reference);
+  expect((await runDoctor(undefined, host)).identity?.skill.state).toBe(
+    "stale",
+  );
+  expect(await installCanonicalSkill(home)).toBe("installed");
+  expect((await runDoctor(undefined, host)).identity?.skill.state).toBe(
+    "aligned",
+  );
+});