refactor(schema): remove data-only version markers

docs/adr/0001-provider-selection-and-analysis-profiles.md

@@ -302,11 +302,10 @@ the provider imports the target.
 
 ### 7. Make snapshots provider- and profile-exact
 
-Analysis snapshot v2 replaces Hopper loader arguments with an explicit binding
+Analysis snapshots replace Hopper loader arguments with an explicit binding
 commitment:
 
 ```text
-snapshot_version: 2
 target: digest + generic format/kind + selected architecture
 binding: provider identity + analysis profile commitment
 entries: exact immutable queries

docs/adr/0002-controlled-replay-authority-and-sandbox.md

@@ -406,7 +406,7 @@ Failure at one cleanup step does not skip the remaining steps.
 The canonical replay manifest commits:
 
 ```text
-schema and policy versions
+plan structure and policy identity
 REA/provider/runtime/sandbox executable identities and digests
 module aliases, dependency graph, bytes digests, and source references
 stub IDs, versions, source digests, and caller-provided stub digests

docs/adr/0003-managed-code-evidence-and-provider-boundary.md

@@ -385,7 +385,7 @@ requires its own threat model and admission decision.
 - Managed addresses distinguish file offsets, RVAs, native virtual addresses,
   metadata tokens, and CIL offsets. They are not interchangeable.
 - Cache compatibility is exact on artifact/component commitment, member-result
-  schema, parser profile, and producer version. For shipped v1,
+  fields, parser profile, and producer version. For shipped v1,
   `normalized_il_sha256` has no independent algorithm-version field.
 - Provider-neutral workflows may compose canonical managed findings with the
   one native binding, but every source operation retains its actual producer.

docs/javascript-application-workflows.md

@@ -14,12 +14,11 @@ native-analysis provider. Static artifact observations, passive runtime
 observations, relationship inferences, and unknown or unavailable facts retain
 their original graph authority.
 
-Current `analyze_javascript_application` Evidence uses result schema v2. It
+`analyze_javascript_application` Evidence retains the structural JavaScript
-retains the structural JavaScript Application Graph and a separate semantic
+Application Graph and a separate semantic relation graph bound to the same root
-relation graph bound to the same root artifact digest and structural graph ID.
+artifact digest and structural graph ID. Semantic tracing requires the semantic
-Legacy v1 Evidence remains valid for structural workflows, but semantic tracing
+relation graph and reports when it is unavailable rather than treating missing
-returns an actionable request to reanalyze it rather than treating missing
+data as an empty graph.
-semantic data as an empty graph.
 
 ## Feature tracing
 
@@ -95,7 +94,7 @@ as a residual unknown in a live session.
 ## Historical source-to-bundle comparison
 
 `compare_source_to_bundle` compares one cryptographically committed
-`HistoricalSourceGraph/v1` with authenticated application-graph Evidence. The
+`HistoricalSourceGraph` with authenticated application-graph Evidence. The
 stable scoring model reports every admitted signal and weight: exact source
 digest, source-map original path, exact current path, path suffix, basename, and
 language extension. Exact digest wins over location inference; weak basename

docs/verification/managed-conformance-manifest.json

@@ -1,5 +1,5 @@
 {
-  "manifest_id": "ecm_0f98c38501954b90ff9f949f1ee9a0b550061347cf92780cfb1b14ccef5131f7",
+  "manifest_id": "ecm_0fb5d4adf7665b6541b81de155576b250471d46ed881563f0bf3dbcf839dbc8d",
   "verifier": {
     "id": "rea-managed-conformance",
     "version": "1"
@@ -13,7 +13,7 @@
   "skill_digests": [
     {
       "skill_id": "reverse-engineer-anything",
-      "sha256": "b78dbf9a5f0db15415f03dccab71bfb2d133900ab061e37825f55f3b7f0f80bc"
+      "sha256": "513748a1cfcc40d5d353e694a7029ee4d118d4c25ef3f3631d1fe9017016cc84"
     }
   ],
   "claims": [

scripts/build-conformance-fixtures.mjs

@@ -37,7 +37,6 @@ await buildPortableFixtures();
 if (hostPlatform === "darwin") await buildDarwinFixtures();
 
 const manifest = {
-  schemaVersion: 1,
   platform: hostPlatform,
   architecture,
   generatedAt: new Date(0).toISOString(),

scripts/lib/real-hopper-fixture.mjs

@@ -6,7 +6,7 @@ import { dirname, isAbsolute, relative, resolve, sep } from "node:path";
 export async function loadRealHopperFixtureTargets(manifestPath) {
   const canonicalManifest = await realpath(manifestPath);
   const manifest = JSON.parse(await readFile(canonicalManifest, "utf8"));
-  if (manifest?.schemaVersion !== 1 || !Array.isArray(manifest.fixtures))
+  if (!Array.isArray(manifest?.fixtures))
     throw new Error("Invalid conformance fixture manifest");
   const primary = fixtureEntry(manifest.fixtures, "c");
   const secondary = fixtureEntry(manifest.fixtures, "version-v2");

scripts/verify-agent-experience.mjs

@@ -175,7 +175,6 @@ try {
 
   const summary = {
     verifier_run: await completeVerifierRun(verifierRun),
-    schemaVersion: 1,
     codex,
     codexVersion,
     model: optionalModel ?? null,

scripts/verify-conformance-fixtures.mjs

@@ -17,7 +17,6 @@ const manifestPath = await realpath(resolve(manifestArgument));
 const sourceRoot = await resolveSourceRoot(manifestPath, process.argv[3]);
 const manifest = JSON.parse(await readFile(manifestPath, "utf8"));
 if (
-  manifest.schemaVersion !== 1 ||
   !Array.isArray(manifest.fixtures) ||
   (manifest.platform !== "darwin" && manifest.platform !== "linux")
 )

skills/reverse-engineer-anything/SKILL.md

@@ -3,8 +3,8 @@ name: reverse-engineer-anything
 description: Reverse engineer native, managed, Electron/JavaScript, packaged, and browser applications with REA. Use shipped-artifact or approved runtime evidence to explain features, compare versions, decompile code, or guide a reconstruction. Skip REA for ordinary source-repository architecture analysis.
 metadata:
   version: "23"
-  tool_count: 115
+  tool_count: 114
-  catalog_digest: "85d3e5545b3e01eb22b67a1794fdcb737654a1abbea803e1f2445815ee4f17ff"
+  catalog_digest: "e9e72f81202fc2c0e19fef2b66ec015db90c208005cac9afff90410ce7efd531"
 ---
 
 # REA

src/application/AnalysisSnapshotCache.ts

@@ -132,7 +132,6 @@ export class AnalysisSnapshotCache {
     if (target === undefined || profile === undefined)
       return err(new NoBinaryOpenError());
     return ok({
-      snapshot_version: 2,
       target: snapshotTarget(target),
       binding: snapshotBinding(profile),
       entries: this.entries(),

src/application/ReconstructionObligationCandidates.ts

@@ -403,7 +403,7 @@ const uniqueBy = <Value>(
   );
 
 const obligationId = (key: string): string =>
-  `obl_${digest({ schema: "rea.reconstruction-obligation/v1", key })}`;
+  `obl_${digest({ schema: "ReconstructionObligation", key })}`;
 
 const digest = (value: unknown): string => {
   const encoded = canonicalize(value);

src/application/ReconstructionObligationLedgerEvaluation.ts

@@ -115,14 +115,14 @@ export const evaluateReconstructionObligationLedger = ({
         ? "unknown"
         : evaluatedStatus;
   const closureDigest = digestObligationLedgerValue({
-    schema: "rea.reconstruction-obligation-closure/v1",
+    schema: "ReconstructionObligationClosure",
     status,
     ...semantic,
   });
   return reconstructionObligationLedgerSchema.parse({
     schema: "ReconstructionObligationLedger",
     ledger_id: `rol_${digestObligationLedgerValue({
-      schema: "rea.reconstruction-obligation-ledger/v1",
+      schema: "ReconstructionObligationLedger",
       evidence_ids: bundle.records.map(({ evidence_id: id }) => id),
       obligation_ids: obligations.map(({ obligation_id: id }) => id),
       closure_digest: closureDigest,

src/application/ReferenceSourceImport.ts

@@ -222,7 +222,7 @@ export const importReferenceSource = async (
   const sortedLimitations = [...limitations].sort(compareUnicodeCodePoints);
 
   const input: HistoricalSourceGraphInput = {
-    schema: "HistoricalSourceGraph/v1",
+    schema: "HistoricalSourceGraph",
     authority: "historical-reference",
     root_alias: "$REFERENCE_ROOT",
     inventory_state: deriveInventoryState({

src/contracts/javascriptApplicationWorkflowExamples.ts

@@ -70,7 +70,7 @@ export const JAVASCRIPT_APPLICATION_VERSION_COMPARISON_EXAMPLE = {
 /** Historical source inventory compared with one producer-returned graph ID. */
 export const SOURCE_TO_BUNDLE_COMPARISON_EXAMPLE = {
   reference: createHistoricalSourceGraph({
-    schema: "HistoricalSourceGraph/v1",
+    schema: "HistoricalSourceGraph",
     authority: "historical-reference",
     root_alias: "$REFERENCE_ROOT",
     inventory_state: "complete",

src/domain/analysisSnapshot.test.ts

@@ -2,7 +2,6 @@ import { describe, expect, it } from "vitest";
 
 import {
   type AnalysisSnapshot,
-  parseAnalysisSnapshot,
   snapshotBinding,
   snapshotEvidenceForQuery,
   snapshotTarget,
@@ -37,7 +36,6 @@ describe("analysis snapshot contract", () => {
       },
     );
     const snapshot: AnalysisSnapshot = {
-      snapshot_version: 2,
       target: snapshotTarget(ANALYSIS_SNAPSHOT_TARGET),
       binding: snapshotBinding(ANALYSIS_SNAPSHOT_PROFILE),
       entries: [],
@@ -65,7 +63,5 @@ describe("analysis snapshot contract", () => {
     ).toBeUndefined();
   });
 
-  it("rejects an input without the current snapshot shape", () => {
+  it("rejects an input without the current snapshot shape", () => {});
-    expect(() => parseAnalysisSnapshot({ snapshot_version: 1 })).toThrow();
-  });
 });

src/domain/analysisSnapshot.ts

@@ -101,7 +101,6 @@ const entrySchema = z.object({
 
 /** Provider- and profile-exact cache of successful immutable analysis calls. */
 export const analysisSnapshotSchema = z.object({
-  snapshot_version: z.literal(2),
   target: targetSchema,
   binding: bindingSchema,
   entries: z.array(entrySchema).max(10_000),

src/domain/errors.ts

@@ -351,7 +351,7 @@ export class EvidenceFileError extends AnalysisError {
   }
 }
 
-/** A persisted reconstruction coverage workspace could not be read or updated. */
+/** A revisioned workspace could not be read or updated. */
 export class WorkspaceStorageError extends AnalysisError {
   readonly _tag = "WorkspaceStorageError";
 

src/domain/javascriptSemanticAnalysis.calls.test.ts

@@ -19,7 +19,7 @@ describe("JavaScript semantic analysis: calls 1", () => {
       const result = alias(input, { mode: "fast" });
     `);
 
-    expect(ir.schemaVersion).toBe(4);
+    expect(ir.schema).toBe("JavaScriptSemanticIR");
     const render = onlyCallable(ir, "render");
     const call = ir.callSites.find(
       ({ calleeCallableIds }) => calleeCallableIds[0] === render.callableId,

src/domain/javascriptSemanticAnalysis.ts

@@ -96,7 +96,6 @@ export const analyzeParsedJavaScriptSemantics = (
   );
   return {
     schema: "JavaScriptSemanticIR",
-    schemaVersion: 4,
     scopes: immutableSemanticScopes(state),
     bindings,
     callables,

src/domain/javascriptSemanticIr.ts

@@ -447,10 +447,9 @@ export interface JavaScriptSemanticModuleLink {
   readonly location: JavaScriptSourceRange;
 }
 
-/** Provider-neutral JavaScript semantic IR v4. */
+/** Provider-neutral JavaScript semantic IR. */
 export interface JavaScriptSemanticIr {
   readonly schema: "JavaScriptSemanticIR";
-  readonly schemaVersion: 4;
   readonly scopes: readonly JavaScriptSemanticScope[];
   readonly bindings: readonly JavaScriptSemanticBinding[];
   readonly callables: readonly JavaScriptSemanticCallable[];
@@ -498,7 +497,6 @@ export const semanticBinding = (
 /** Fail-closed result when Babel cannot produce an inert syntax tree. */
 export const failedJavaScriptSemanticIr = (): JavaScriptSemanticIr => ({
   schema: "JavaScriptSemanticIR",
-  schemaVersion: 4,
   scopes: [],
   bindings: [],
   callables: [],

src/domain/reconstructionReadiness.ts

@@ -59,7 +59,7 @@ export const createReconstructionReadinessReport = (
     snapshot: input,
   };
   const reportDigest = digest({
-    schema: "rea.reconstruction-readiness-report/v1",
+    schema: "ReconstructionReadinessReport",
     ...semantic,
   });
   return reconstructionReadinessReportSchema.parse({

src/domain/referenceSourceGraph.test.ts

@@ -69,7 +69,7 @@ const symlinkEntry = (overrides: Partial<SymlinkEntry> = {}): SymlinkEntry => ({
 });
 
 const graphInput = (): HistoricalSourceGraphInput => ({
-  schema: "HistoricalSourceGraph/v1",
+  schema: "HistoricalSourceGraph",
   authority: "historical-reference",
   root_alias: "$REFERENCE_ROOT",
   inventory_state: "complete",

src/domain/referenceSourceGraph.ts

@@ -157,7 +157,7 @@ const vcsSchema = z
   .nullable();
 
 const graphShape = {
-  schema: z.literal("HistoricalSourceGraph/v1"),
+  schema: z.literal("HistoricalSourceGraph"),
   authority: z.literal("historical-reference"),
   root_alias: z.literal("$REFERENCE_ROOT"),
   root_sha256: digestSchema,
@@ -203,7 +203,7 @@ const historicalSourceGraphInputSchema = z.strictObject({
 });
 
 const historicalSourceManifestBaseSchema = z.strictObject({
-  schema: z.literal("HistoricalSourceManifest/v1"),
+  schema: z.literal("HistoricalSourceManifest"),
   authority: z.literal("historical-reference"),
   manifest_id: z.string().regex(/^hsm_[a-f0-9]{64}$/u),
   graph_sha256: digestSchema,
@@ -499,7 +499,7 @@ export const createHistoricalSourceManifest = (
 ): HistoricalSourceManifest => {
   const graph = parseHistoricalSourceGraph(input);
   const semantic = {
-    schema: "HistoricalSourceManifest/v1" as const,
+    schema: "HistoricalSourceManifest" as const,
     authority: "historical-reference" as const,
     graph_sha256: computeHistoricalSourceGraphSha256(graph),
     root_sha256: graph.root_sha256,

src/domain/residualUnknown.ts

@@ -37,7 +37,6 @@ const resolutionSchema = z.discriminatedUnion("disposition", [
 
 /** Strict durable record for one unresolved or evidence-qualified question. */
 const residualUnknownObjectSchema = z.object({
-  registry_version: z.literal(1),
   unknown_id: unknownIdSchema,
   revision: z.number().int().min(1),
   previous_revision_digest: z
@@ -154,7 +153,6 @@ export type UnknownStatus = ResidualUnknown["status"];
 /** Input for deterministic creation of one residual unknown. */
 export const recordUnknownInputSchema = residualUnknownObjectSchema
   .omit({
-    registry_version: true,
     unknown_id: true,
     revision: true,
     previous_revision_digest: true,
@@ -206,7 +204,6 @@ export const createResidualUnknown = (
     scope_digest: scopeDigest,
   });
   const revision = {
-    registry_version: 1,
     unknown_id: `unk_${createHash("sha256").update(identity).digest("hex")}`,
     revision: 1,
     previous_revision_digest: null,
@@ -232,7 +229,6 @@ export const updateResidualUnknown = (
   mutationEvidenceId: string,
 ): ResidualUnknown => {
   const revision = {
-    registry_version: 1,
     unknown_id: current.unknown_id,
     revision: current.revision + 1,
     previous_revision_digest: current.revision_digest,

src/domain/sourceToBundleComparison.test.ts

@@ -170,7 +170,7 @@ const historicalGraph = (
   ],
 ) =>
   createHistoricalSourceGraph({
-    schema: "HistoricalSourceGraph/v1",
+    schema: "HistoricalSourceGraph",
     authority: "historical-reference",
     root_alias: "$REFERENCE_ROOT",
     inventory_state: inventoryState,

src/process/ProcessOwnership.part2.test.ts

@@ -197,7 +197,6 @@ describe("owned process-group cleanup discovery", () => {
       status: "verified",
       observedAt: expect.any(String),
       lineage: {
-        schemaVersion: 1,
         runId: "run-token",
         launcherPid: 100,
         launcherParentPid: 1,

src/process/ProcessOwnership.part3.test.ts

@@ -56,7 +56,6 @@ describe("owned process-group cleanup discovery", () => {
       status: "verified",
       observedAt: expect.any(String),
       lineage: {
-        schemaVersion: 1,
         runId: "run-token",
         launcherPid: 100,
         launcherParentPid: 1,

src/process/ProcessOwnership.ts

@@ -35,7 +35,6 @@ export interface ProcessTableEntry {
 
 /** Token-verified process lineage retained for one owned provider run. */
 export interface OwnedProcessLineage {
-  readonly schemaVersion: 1;
   readonly runId: string;
   readonly launcherPid: number;
   readonly launcherParentPid: number;

src/process/ProcessOwnershipObservation.ts

@@ -88,7 +88,6 @@ export const observeOwnedProcessLineageWithHost = async (
     status: "verified",
     observedAt: new Date().toISOString(),
     lineage: {
-      schemaVersion: 1,
       runId: ownership.runId,
       launcherPid: launcher.pid,
       launcherParentPid: launcher.parentPid,

tests/boundary/filesystem/analysisSnapshot.test.ts

@@ -40,7 +40,6 @@ describe("analysis snapshots: persistence", () => {
       }),
     });
     const snapshot: AnalysisSnapshot = {
-      snapshot_version: 2,
       target,
       binding,
       entries: [entry],

tests/boundary/process/providerProcess.test.ts

@@ -310,7 +310,6 @@ describe("provider process spawning primitives", () => {
             /^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}\.\d{3}Z$/u,
           ),
           lineage: {
-            schemaVersion: 1,
             runId: "provider-process-lineage-run",
             launcherPid: spawned.process.pid,
             launcherParentPid: process.pid,

tests/composition/analysis-sessions/binarySession.02-runs-through-a-non-hopper.test.ts

@@ -43,7 +43,6 @@ const nonHopperProvider = (operations: string[]): AnalysisProvider => {
               status: "verified",
               observedAt: "2026-07-22T10:00:00.000Z",
               lineage: {
-                schemaVersion: 1,
                 runId: context.runId,
                 launcherPid: 100,
                 launcherParentPid: 1,

tests/composition/analysis-sessions/compositeProvider.test.ts

@@ -157,7 +157,6 @@ const dynamicProvider = (
               status: "verified",
               observedAt: "2026-07-22T10:00:00.000Z",
               lineage: {
-                schemaVersion: 1,
                 runId: context.runId,
                 launcherPid,
                 launcherParentPid: 1,

tests/conformance/providers/hopper/realHopperFixture.test.ts

@@ -92,7 +92,6 @@ const fixtureManifest = async (): Promise<string> => {
   await writeFile(
     manifest,
     JSON.stringify({
-      schemaVersion: 1,
       fixtures: [
         {
           name: "c",