fix(settings): classify caller-selected limits as parameter updates

analysis_timeout_ms, max_heap_mb, and command_timeout_ms keep the source chosen by the caller, the runtime override, or the built-in default. A request value reports update_mode parameter because update_analysis_settings cannot change that call.

src/application/javascript/JavaScriptArtifactReconstruction.ts

@@ -1,6 +1,7 @@
 import { discoverJavaScriptPreloadPaths } from "./JavaScriptPreloadDiscovery.js";
 import { artifactNameForClassification } from "../../domain/artifactNameSelection.js";
 import type { AnalysisSettingValues } from "../../domain/analysisSettings.js";
+import { selectedAnalysisSetting } from "../../domain/analysisSettingDefinitions.js";
 import { absoluteCallerPath } from "../../filesystem/callerPath.js";
 import {
   DEFAULT_ASAR_HEADER_ADMISSION,
@@ -181,18 +182,24 @@ export const reconstructJavaScriptArtifact = async (
           ? {}
           : { fileNodes: input.max_semantic_nodes_per_file }),
       });
+      const heap = selectedAnalysisSetting(
+        input.max_heap_mb,
+        overrides?.["javascript.max_heap_mb"],
+        JAVASCRIPT_ANALYSIS_RESOURCE_DEFAULTS.heapMb,
+      );
+      const timeout = selectedAnalysisSetting(
+        input.analysis_timeout_ms,
+        overrides?.["javascript.analysis_timeout_ms"],
+        JAVASCRIPT_ANALYSIS_RESOURCE_DEFAULTS.timeoutMs,
+      );
       const sourceLimits = {
         ...(input.semantic_precision === undefined
           ? {}
           : { semanticPrecision: input.semantic_precision }),
-        heapMb:
-          input.max_heap_mb ??
-          overrides?.["javascript.max_heap_mb"] ??
-          JAVASCRIPT_ANALYSIS_RESOURCE_DEFAULTS.heapMb,
-        timeoutMs:
-          input.analysis_timeout_ms ??
-          overrides?.["javascript.analysis_timeout_ms"] ??
-          JAVASCRIPT_ANALYSIS_RESOURCE_DEFAULTS.timeoutMs,
+        heapMb: heap.value,
+        heapSource: heap.source,
+        timeoutMs: timeout.value,
+        timeoutSource: timeout.source,
       };
       const preloads = await discoverJavaScriptPreloadPaths(
         files,

src/application/wasm/WasmArtifactPort.ts

@@ -15,6 +15,8 @@ export type WasmArtifactExecution = Omit<AnalysisExecution, "subject"> & {
 /** Effective operation budget, separate from caller-authored Evidence parameters. */
 export interface WasmArtifactExecutionOptions extends ExecutionOptions {
   readonly commandTimeoutMs?: number;
+  /** Selection owner for `commandTimeoutMs`. Absent when the caller did not record it. */
+  readonly commandTimeoutSource?: "default" | "runtime" | "request" | undefined;
 }
 
 /** Replaceable offline WASM inspection engine, independent of target execution and network clients. */

src/application/wasm/WasmArtifactService.test.ts

@@ -240,6 +240,7 @@ it("gives cancellation precedence over malformed raw input", async () => {
 it("uses runtime defaults only for omitted budgets, preserving explicit input and reset", async () => {
   const settings = new AnalysisSettings({});
   const accepted: number[] = [];
+  const sources: (string | undefined)[] = [];
   const authored: (number | undefined)[] = [];
   const service = new WasmArtifactService(
     {
@@ -248,6 +249,7 @@ it("uses runtime defaults only for omitted budgets, preserving explicit input an
         const value = wasmArtifactFixture();
         value.tool_profile.timeout_ms = options!.commandTimeoutMs!;
         accepted.push(options!.commandTimeoutMs!);
+        sources.push(options!.commandTimeoutSource);
         authored.push(input.command_timeout_ms);
         return ok(wasmArtifactExecution(value));
       },
@@ -275,6 +277,7 @@ it("uses runtime defaults only for omitted budgets, preserving explicit input an
   });
   expect((await settings.run(() => service.inspect({ path }))).ok).toBe(true);
   expect(accepted).toEqual([123000, 42000, 30000]);
+  expect(sources).toEqual(["runtime", "request", "default"]);
   expect(authored).toEqual([undefined, 42000, undefined]);
 });
 

src/application/wasm/WasmArtifactService.ts

@@ -1,4 +1,5 @@
 import type { AnalysisSettingsReader } from "../../domain/analysisSettings.js";
+import { selectedAnalysisSetting } from "../../domain/analysisSettingDefinitions.js";
 import { constants as bufferConstants } from "node:buffer";
 import type { ExecutionOptions } from "../AnalysisProvider.js";
 import {
@@ -78,13 +79,15 @@ export class WasmArtifactService {
           ),
         );
     }
-    const timeout =
-      input.value.command_timeout_ms ??
-      this.settings?.().overrides["wasm.command_timeout_ms"] ??
-      DEFAULT_WASM_COMMAND_TIMEOUT_MS;
+    const timeout = selectedAnalysisSetting(
+      input.value.command_timeout_ms,
+      this.settings?.().overrides["wasm.command_timeout_ms"],
+      DEFAULT_WASM_COMMAND_TIMEOUT_MS,
+    );
     const inspected = await this.provider.inspect(input.value, {
       ...options,
-      commandTimeoutMs: timeout,
+      commandTimeoutMs: timeout.value,
+      commandTimeoutSource: timeout.source,
     });
     if (!inspected.ok) return inspected;
     const execution = inspected.value;
@@ -108,7 +111,7 @@ export class WasmArtifactService {
       !report.success ||
       report.data.artifact.path !== input.value.path ||
       execution.subject.path !== input.value.path ||
-      report.data.tool_profile.timeout_ms !== timeout ||
+      report.data.tool_profile.timeout_ms !== timeout.value ||
       report.data.tool_profile.output_budget_bytes !==
         wasmResourceLimits(input.value).outputBytes ||
       !wasmArtifactMatchesSubject(report.data.artifact, execution.subject) ||

src/domain/analysisErrorProjection.test.ts

@@ -1530,11 +1530,25 @@ describe("analysis error projection: caller lifetime", () => {
       expect.objectContaining({
         setting: "wasm.command_timeout_ms",
         source: "request",
+        update_mode: "parameter",
         parameter: "command_timeout_ms",
         applies_at: "next_invocation",
         scope: "rea-invocation",
       }),
     );
+    expect(
+      analysisSettingLimit("wasm.command_timeout_ms", 100, "runtime"),
+    ).toMatchObject({ source: "runtime", update_mode: "runtime" });
+    expect(
+      analysisSettingLimit("javascript.max_heap_mb", 128, "request"),
+    ).toMatchObject({
+      source: "request",
+      update_mode: "parameter",
+      parameter: "max_heap_mb",
+    });
+    expect(
+      analysisSettingLimit("javascript.analysis_timeout_ms", 1, "default"),
+    ).toMatchObject({ source: "default", update_mode: "runtime" });
     expect(
       projectAnalysisError(error, "invocation").details?.limit,
     ).not.toHaveProperty("environment");

src/domain/analysisSettingDefinitions.ts

@@ -333,6 +333,23 @@ export const analysisSettingValueSchema = (id: AnalysisSettingId) => {
     ? number.nullable()
     : number;
 };
+/**
+ * Caller argument, then the accepted runtime override, then the built-in
+ * default. The third value is that default, not a launch-environment seed.
+ */
+export const selectedAnalysisSetting = (
+  request: number | undefined,
+  override: number | undefined,
+  fallback: number,
+): {
+  readonly value: number;
+  readonly source: "default" | "runtime" | "request";
+} => {
+  if (request !== undefined) return { value: request, source: "request" };
+  if (override !== undefined) return { value: override, source: "runtime" };
+  return { value: fallback, source: "default" };
+};
+
 /** Project one owner's accepted budget, including the explicit per-call precedence. */
 export const analysisSettingLimit = (
   setting: AnalysisSettingId,
@@ -350,7 +367,7 @@ export const analysisSettingLimit = (
     applies_at: definition.appliesAt,
     agent_editable: true,
     scope: "rea-runtime",
-    update_mode: definition.updateMode,
+    update_mode: source === "request" ? "parameter" : definition.updateMode,
     pending_restart: false,
     ...(definition.parameter === undefined
       ? {}

src/domain/analysisSettings.ts

@@ -29,8 +29,8 @@ export type AnalysisSettingsReader = () => AnalysisSettingsSnapshot;
 /**
  * Whether `update_analysis_settings` can change the active value.
  * `runtime` applies inside this process. `restart` stays at the value this
- * process already started with. Caller-selected parameters use `parameter`
- * on their own facts; they are not analysis settings.
+ * process already started with. A limit fact uses `parameter` when this call
+ * supplied the value; the setting definition itself stays `runtime`.
  */
 export type AnalysisSettingUpdateMode = "runtime" | "restart";
 
@@ -45,7 +45,7 @@ export interface AnalysisSettingLimit {
   readonly applies_at: "next_operation" | "next_worker" | "next_startup";
   readonly agent_editable: true;
   readonly scope: "rea-runtime";
-  readonly update_mode: AnalysisSettingUpdateMode;
+  readonly update_mode: AnalysisSettingUpdateMode | "parameter";
   /**
    * True only when a configured value is not the one this process is using.
    * The reported effective value is active, so limit errors leave this false.

src/domain/javascript/javascriptSourceAnalysis.ts

@@ -41,7 +41,21 @@ export interface JavaScriptSourceAnalysisFailure {
 export interface JavaScriptSourceAnalysisLimits {
   readonly semanticPrecision?: JavaScriptSemanticPrecisionInput;
   readonly heapMb: number;
+  /** Where `heapMb` was selected. Absent when the caller did not record it. */
+  readonly heapSource?:
+    | "default"
+    | "setting"
+    | "runtime"
+    | "request"
+    | undefined;
   readonly timeoutMs: number;
+  /** Where `timeoutMs` was selected. Absent when the caller did not record it. */
+  readonly timeoutSource?:
+    | "default"
+    | "setting"
+    | "runtime"
+    | "request"
+    | undefined;
 }
 
 /** Sequential source-analysis authority with independently verified cleanup. */

src/javascript/analysis/JavaScriptAnalysisWorker.ts

@@ -951,7 +951,7 @@ export class JavaScriptAnalysisWorker {
         limit: analysisSettingLimit(
           "javascript.max_heap_mb",
           this.limits.heapMb,
-          undefined,
+          this.limits.heapSource,
         ),
         remediationAction: javaScriptWorkerHeapRemediation(this.limits.heapMb),
       },
@@ -1150,7 +1150,7 @@ export class JavaScriptAnalysisWorker {
           limit: analysisSettingLimit(
             "javascript.analysis_timeout_ms",
             this.limits.timeoutMs,
-            undefined,
+            this.limits.timeoutSource,
           ),
           capturedOutput: this.#captured(),
           userMessage: `JavaScript source analysis reached its ${String(this.limits.timeoutMs)}ms per-source server/provider deadline (analysis_timeout_ms), not the MCP client deadline.`,
@@ -1185,7 +1185,7 @@ export class JavaScriptAnalysisWorker {
                 limit: analysisSettingLimit(
                   "javascript.max_heap_mb",
                   this.limits.heapMb,
-                  undefined,
+                  this.limits.heapSource,
                 ),
               }
             : {}),

src/wasm/WabtArtifactProvider.test.ts

@@ -1223,7 +1223,15 @@ it("enforces a selected command deadline and completes a corrected retry after c
   if (timed.ok) throw new Error("Selected 20 ms deadline was not enforced");
   expect(projectAnalysisError(timed.error)).toMatchObject({
     code: "provider_timeout",
-    details: { timeout_ms: 20 },
+    details: {
+      timeout_ms: 20,
+      limit: {
+        setting: "wasm.command_timeout_ms",
+        effective_value: 20,
+        source: "request",
+        update_mode: "parameter",
+      },
+    },
     remediation: { action: expect.stringContaining("command_timeout_ms") },
   });
   expect(timed.error.cleanupIncomplete).toBe(false);

src/wasm/WabtArtifactProvider.ts

@@ -230,6 +230,10 @@ export class WabtArtifactProvider implements WasmArtifactPort {
       input.command_timeout_ms ??
       options?.commandTimeoutMs ??
       DEFAULT_WASM_COMMAND_TIMEOUT_MS;
+    const commandTimeoutSource =
+      input.command_timeout_ms !== undefined
+        ? "request"
+        : options?.commandTimeoutSource;
     try {
       if (options?.signal?.aborted)
         throw new AnalysisCancelledError(OPERATION, {
@@ -713,6 +717,9 @@ export class WabtArtifactProvider implements WasmArtifactPort {
         phase === "artifact" ? artifactInput.path : input.path,
         {
           commandTimeoutMs,
+          ...(commandTimeoutSource === undefined
+            ? {}
+            : { commandTimeoutSource }),
           limits,
           inputField: artifactInput.field,
           observedOutput: capturedOutput,

src/wasm/WabtFailures.test.ts

@@ -122,6 +122,24 @@ it.each([1234, 2_147_483_647])(
       },
       recovery: { kind: "inspect_timeout_state", timeout_ms: commandTimeoutMs },
     });
+    expect(
+      projectAnalysisError(
+        wabtFailure(
+          new OwnedCommandFailure("timeout", "deadline"),
+          "producer",
+          "/module.wasm",
+          { commandTimeoutMs, commandTimeoutSource: "request" },
+        ),
+      ),
+    ).toMatchObject({
+      details: {
+        limit: {
+          source: "request",
+          update_mode: "parameter",
+          effective_value: commandTimeoutMs,
+        },
+      },
+    });
   },
 );
 

src/wasm/WabtFailures.ts

@@ -60,6 +60,12 @@ export type WabtVersionProbe = {
 
 type WabtFailureContext = {
   readonly commandTimeoutMs: number;
+  readonly commandTimeoutSource?:
+    | "default"
+    | "setting"
+    | "runtime"
+    | "request"
+    | undefined;
   readonly limits?: WasmResourceLimits;
   readonly versionProbe?: WabtVersionProbe;
   readonly inputField?: readonly (string | number)[];
@@ -179,13 +185,17 @@ const classifyWabtFailure = (
     // Classify once before cleanup takes precedence, so the primary remains actionable.
     const timeoutMs =
       execution?.commandTimeoutMs ?? DEFAULT_WASM_COMMAND_TIMEOUT_MS;
+    const timeoutSource =
+      execution?.commandTimeoutMs === undefined
+        ? "default"
+        : execution.commandTimeoutSource;
     const timeout =
       cause.reason === "timeout"
         ? new AnalysisTimeoutError("inspect_wasm_artifact", timeoutMs, {
             limit: analysisSettingLimit(
               "wasm.command_timeout_ms",
               timeoutMs,
-              undefined,
+              timeoutSource,
             ),
             ...options,
             // The cleanup wrapper retains output once; its nested primary needs only recovery facts.

tests/boundary/mcp/javascriptAnalysisResources.test.ts

@@ -250,13 +250,14 @@ it("returns a directly usable partial analysis reference for an oversized timeou
       limit: {
         setting: "javascript.analysis_timeout_ms",
         effective_value: 1,
+        source: "request",
         parameter: "analysis_timeout_ms",
         unit: "ms",
         minimum: 1,
         maximum: 2_147_483_647,
         applies_at: "next_operation",
         agent_editable: true,
-        update_mode: "runtime",
+        update_mode: "parameter",
         pending_restart: false,
       },
     });