diff --git a/src/application/javascript/JavaScriptApplicationService.test.ts b/src/application/javascript/JavaScriptApplicationService.test.ts
index c76796c02..8529ff333 100644
--- a/src/application/javascript/JavaScriptApplicationService.test.ts
+++ b/src/application/javascript/JavaScriptApplicationService.test.ts
@@ -8,6 +8,7 @@ import { z } from "zod";
 import { createTestTempDirectory } from "../../../tests/fixtures/temporaryDirectory.js";
 import { projectAnalysisError } from "../../domain/analysisErrorProjection.js";
 import { analyzeJavaScriptApplication } from "./JavaScriptApplicationService.js";
+import { compareApplicationVersionsEvidence } from "./JavaScriptApplicationWorkflowService.js";
 
 describe("JavaScript application failure diagnostics", () => {
   it("identifies the rejected result field in caller-visible diagnostics", async () => {
@@ -122,6 +123,9 @@ describe("JavaScript application failure diagnostics", () => {
   );
 });
 
+const CONTRADICTION_LIMITATION =
+  "Observed bytes of 1 artifact file(s) contradict declared integrity and are untrusted; contradicted nested archives were not expanded: addon.node.";
+
 describe("JavaScript application artifact integrity", () => {
   it("analyzes a signed-after-packaging native module only when the mismatch is recorded", async () => {
     const root = await createTestTempDirectory("rea-js-integrity-");
@@ -169,9 +173,27 @@ describe("JavaScript application artifact integrity", () => {
           trust: "observed-untrusted",
         },
       ],
-      limitations: expect.arrayContaining([
-        "1 artifact file(s) contradict declared integrity; their observed bytes are untrusted, and contradicted nested archives were not expanded.",
-      ]),
+      graph: { coverage: { status: "partial" } },
+      limitations: expect.arrayContaining([CONTRADICTION_LIMITATION]),
+      semantic_graph: {
+        limitations: expect.arrayContaining([CONTRADICTION_LIMITATION]),
+      },
+    });
+
+    // Workflows built on the recorded graph inherit its partial coverage.
+    const clean = await analyzeJavaScriptApplication({
+      input_path: source,
+      format: "directory",
+    });
+    if (!clean.ok) throw new Error("Expected clean analysis");
+    const comparison = compareApplicationVersionsEvidence({
+      left: clean.value,
+      right: recorded.value,
+    });
+    expect(comparison.ok).toBe(true);
+    if (!comparison.ok) throw new Error("Expected comparison");
+    expect(comparison.value.normalized_result).toMatchObject({
+      coverage: { status: "partial", right_graph_status: "partial" },
     });
   });
 });
diff --git a/src/application/javascript/JavaScriptApplicationService.ts b/src/application/javascript/JavaScriptApplicationService.ts
index 8ff28e816..fd845f798 100644
--- a/src/application/javascript/JavaScriptApplicationService.ts
+++ b/src/application/javascript/JavaScriptApplicationService.ts
@@ -60,18 +60,10 @@ export const analyzeJavaScriptApplicationValidated = async (
       options.signal,
     );
     const { electron_summary: summary, ...application } = reconstructed;
-    const contradictions = reconstructed.integrity_contradictions.length;
     const result = javascriptApplicationAnalysisResultSchema.parse({
       ...application,
       summary,
-      limitations: [
-        ...reconstructed.graph.limitations,
-        ...(contradictions === 0
-          ? []
-          : [
-              `${String(contradictions)} artifact file(s) contradict declared integrity; their observed bytes are untrusted, and contradicted nested archives were not expanded.`,
-            ]),
-      ],
+      limitations: reconstructed.graph.limitations,
     });
     await options.progress?.report({
       phase: "analyze_javascript_application",
diff --git a/src/application/javascript/JavaScriptArtifactGraphBuilder.ts b/src/application/javascript/JavaScriptArtifactGraphBuilder.ts
index 8c187e581..892454aef 100644
--- a/src/application/javascript/JavaScriptArtifactGraphBuilder.ts
+++ b/src/application/javascript/JavaScriptArtifactGraphBuilder.ts
@@ -92,6 +92,7 @@ const graphCoverage = (context: JavaScriptArtifactGraphContext) => {
       javascript !== null && javascript.parse_status === "partial",
   );
   const unknownGap =
+    context.snapshot.integrity_contradictions.length > 0 ||
     context.analysis.parse_failures > 0 ||
     context.fileSet.invalid_utf8_files > 0 ||
     sourceMapPolicyGap ||
@@ -103,6 +104,20 @@ const graphCoverage = (context: JavaScriptArtifactGraphContext) => {
   return completeApplicationCoverage();
 };
 
+/**
+ * Disclose recorded integrity contradictions wherever the application graph
+ * is consumed; the graph is also partial, so comparisons and traces built on
+ * it do not claim completeness.
+ */
+export const integrityContradictionLimitations = (
+  snapshot: Pick<ArtifactInventorySnapshot, "integrity_contradictions">,
+): string[] =>
+  snapshot.integrity_contradictions.length === 0
+    ? []
+    : [
+        `Observed bytes of ${String(snapshot.integrity_contradictions.length)} artifact file(s) contradict declared integrity and are untrusted; contradicted nested archives were not expanded: ${snapshot.integrity_contradictions.map(({ logical_path: path }) => path).join(", ")}.`,
+      ];
+
 const graphLimitations = (
   context: JavaScriptArtifactGraphContext,
   coverage: "complete" | "partial" | "unknown" | "unavailable",
@@ -124,6 +139,7 @@ const graphLimitations = (
   );
   return [
     ...context.analysis.limitations,
+    ...integrityContradictionLimitations(context.snapshot),
     "CommonJS and ESM binding relationships were recovered from inert syntax and resolved only within the inventoried artifact container.",
     "Webpack/Rspack factories were recovered from AST literals; REA did not invoke push handlers or bundle bootstrap code.",
     "Static imports, entrypoints, workers, endpoints, and storage relationships do not prove runtime execution.",
diff --git a/src/application/javascript/JavaScriptArtifactReconstruction.ts b/src/application/javascript/JavaScriptArtifactReconstruction.ts
index 84dfa7628..64dc153c4 100644
--- a/src/application/javascript/JavaScriptArtifactReconstruction.ts
+++ b/src/application/javascript/JavaScriptArtifactReconstruction.ts
@@ -12,7 +12,10 @@ import type { ElectronBoundarySummary } from "../../domain/javascriptApplication
 import type { IntegrityContradiction } from "../../domain/artifactGraph.js";
 import { analyzeJavaScriptArtifactFiles } from "./JavaScriptArtifactAnalysis.js";
 import { readJavaScriptArtifactFiles } from "./JavaScriptArtifactFiles.js";
-import { buildJavaScriptArtifactGraph } from "./JavaScriptArtifactGraphBuilder.js";
+import {
+  buildJavaScriptArtifactGraph,
+  integrityContradictionLimitations,
+} from "./JavaScriptArtifactGraphBuilder.js";
 import {
   javascriptArtifactReconstructionInputSchema,
   type JavaScriptArtifactReconstructionInput,
@@ -75,6 +78,7 @@ export const reconstructJavaScriptArtifact = async (
       rootArtifactSha256: snapshot.manifest.root_sha256,
       applicationGraph: graph,
       analysis,
+      sourceLimitations: integrityContradictionLimitations(snapshot),
     });
     return {
       input_path: path,
diff --git a/src/application/javascript/JavaScriptSemanticGraphBuilder.ts b/src/application/javascript/JavaScriptSemanticGraphBuilder.ts
index 7f36a77d1..827801918 100644
--- a/src/application/javascript/JavaScriptSemanticGraphBuilder.ts
+++ b/src/application/javascript/JavaScriptSemanticGraphBuilder.ts
@@ -58,6 +58,8 @@ interface BuilderInput {
     "graph_id" | "nodes"
   >;
   readonly analysis: JavaScriptArtifactAnalysis;
+  /** Source facts the semantic graph inherits, such as integrity contradictions. */
+  readonly sourceLimitations?: readonly string[];
 }
 
 interface FileContext extends SemanticFlowProjectionContext {
@@ -79,6 +81,7 @@ export const buildJavaScriptSemanticGraph = ({
   rootArtifactSha256,
   applicationGraph,
   analysis,
+  sourceLimitations = [],
 }: BuilderInput): JavaScriptSemanticGraph => {
   const state = emptyState(applicationGraph);
   const fingerprints: JavaScriptSemanticGraph["fingerprints"][number][] = [];
@@ -119,6 +122,7 @@ export const buildJavaScriptSemanticGraph = ({
       })),
     },
     limitations: [
+      ...sourceLimitations,
       "The semantic graph contains static syntax observations and conservative relationship candidates; it does not claim runtime execution.",
       "Local data flow does not claim control-flow-sensitive reaching definitions or arbitrary dynamic property resolution.",
       "Promise ownership covers explicit unshadowed Promise construction, static factories, aggregation, chaining, and await syntax only.",
diff --git a/src/domain/analysisErrorPresentation.ts b/src/domain/analysisErrorPresentation.ts
index 41233e32c..0eaa65a1a 100644
--- a/src/domain/analysisErrorPresentation.ts
+++ b/src/domain/analysisErrorPresentation.ts
@@ -130,7 +130,7 @@ export const analysisErrorUserMessage = (error: AnalysisError): string => {
     return error.reason === "integrity" &&
       error.artifactDetails !== undefined &&
       INTEGRITY_POLICY_OPERATIONS.has(error.operation)
-      ? "Artifact bytes contradict their declared integrity. If that is expected, such as an unpacked native module signed after packaging, rerun with integrity_policy record-and-continue to keep the mismatch as an untrusted contradiction; otherwise get a fresh copy."
+      ? "Artifact bytes contradict their declared integrity. If that is expected, such as an unpacked native module signed after packaging, rerun with the record-and-continue integrity policy (integrity_policy in MCP, --integrity-policy on the CLI) to keep the mismatch as an untrusted contradiction; otherwise get a fresh copy."
       : artifactMessage(error.reason);
   if (error instanceof EvidenceReferenceError)
     return error.reason === "missing"
diff --git a/tests/boundary/mcp/artifactMcp.test.ts b/tests/boundary/mcp/artifactMcp.test.ts
index 5ae6eec08..d44135a83 100644
--- a/tests/boundary/mcp/artifactMcp.test.ts
+++ b/tests/boundary/mcp/artifactMcp.test.ts
@@ -91,7 +91,7 @@ it.each([
 );
 
 const INTEGRITY_REMEDIATION =
-  "Artifact bytes contradict their declared integrity. If that is expected, such as an unpacked native module signed after packaging, rerun with integrity_policy record-and-continue to keep the mismatch as an untrusted contradiction; otherwise get a fresh copy.";
+  "Artifact bytes contradict their declared integrity. If that is expected, such as an unpacked native module signed after packaging, rerun with the record-and-continue integrity policy (integrity_policy in MCP, --integrity-policy on the CLI) to keep the mismatch as an untrusted contradiction; otherwise get a fresh copy.";
 
 const artifactInventoryResultSchema = z.object({
   occurrences: z.array(