agent-threat-rules 4.1.5 → 4.2.1

package/dist/adapters/openshell-filter.d.ts

@@ -3,7 +3,10 @@
  *
  * Implements the external content-filter contract proposed in
  * NVIDIA/OpenShell#1272 ("L7 content inspection hooks — scriptable
- * request/response filtering"): the OpenShell *supervisor* (outside the agent
+ * request/response filtering"). That proposal was closed as not planned on
+ * 2026-06-11 (OpenShell's maintainers pointed to their middleware RFC,
+ * NVIDIA/OpenShell#1733), so no OpenShell release runs this filter. The
+ * contract: the OpenShell *supervisor* (outside the agent
  * sandbox) runs this as a script against L7 request/response bodies. The body
  * arrives on stdin; the script signals the verdict via exit code:
  *
@@ -13,10 +16,14 @@
  *
  * Two run modes:
  *   one-shot (default): read the whole body from stdin, evaluate, exit.
- *       Matches the #1272 contract literally. Cold-starts the engine per call.
+ *       Matches the #1272 contract literally. Cold-starts the engine per call:
+ *       starting Node, loading the rule set and compiling its patterns take
+ *       hundreds of milliseconds to about a second.
  *   serve (--serve):    read NDJSON requests line-by-line from stdin and write
  *       one NDJSON verdict per line. Loads the rule set ONCE, so per-request
- *       latency is just regex evaluation (sub-ms). Production path for a
+ *       latency is just regex evaluation: a median of about a millisecond for
+ *       a short body, tens of milliseconds for a multi-kilobyte one
+ *       (scripts/bench-evaluate-latency.ts). Intended path for a
  *       persistent guard service (cf. NVIDIA/OpenShell#1733 RFC 0005). A bad
  *       line (or an engine error) yields a per-line error verdict and the
  *       stream continues — one malformed body cannot take the inspector offline.

package/dist/adapters/openshell-filter.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"openshell-filter.d.ts","sourceRoot":"","sources":["../../src/adapters/openshell-filter.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8CG;AAMH,qFAAqF;AACrF,MAAM,MAAM,SAAS,GAAG,SAAS,GAAG,UAAU,CAAC;AAE/C,mDAAmD;AACnD,MAAM,MAAM,QAAQ,GAAG,OAAO,GAAG,MAAM,CAAC;AAmBxC,MAAM,WAAW,aAAa;IAC5B,oFAAoF;IACpF,QAAQ,CAAC,SAAS,EAAE,SAAS,CAAC;IAC9B,gFAAgF;IAChF,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,wFAAwF;IACxF,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAC3B,wEAAwE;IACxE,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC;CAC5B;AAED;;;;GAIG;AACH,MAAM,WAAW,OAAO;IACtB,QAAQ,CAAC,aAAa,EAAE,MAAM,CAAC;IAC/B,QAAQ,CAAC,cAAc,EAAE,MAAM,CAAC;IAChC,QAAQ,CAAC,cAAc,EAAE,MAAM,CAAC;IAChC,QAAQ,CAAC,gBAAgB,EAAE,MAAM,CAAC;IAClC,QAAQ,CAAC,mBAAmB,EAAE,MAAM,CAAC;IACrC,QAAQ,CAAC,4BAA4B,EAAE,MAAM,CAAC;CAC/C;AAED,MAAM,WAAW,aAAa;IAC5B,QAAQ,CAAC,QAAQ,EAAE,QAAQ,CAAC;IAC5B,QAAQ,CAAC,QAAQ,EAAE,SAAS,OAAO,EAAE,CAAC;CACvC;AAmCD;;;GAGG;AACH,qBAAa,eAAe;IAKd,OAAO,CAAC,QAAQ,CAAC,OAAO;IAJpC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAY;IACnC,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAS;IAClC,OAAO,CAAC,WAAW,CAAgC;gBAEtB,OAAO,EAAE,aAAa;IAKnD,kEAAkE;IAClE,OAAO,CAAC,YAAY;IAKpB;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,aAAa,CAAC;CAmBpD;AAID,oFAAoF;AACpF,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,SAAS,GAAG,SAAS,CAGjE;AAOD,sEAAsE;AACtE,wBAAgB,cAAc,CAAC,IAAI,EAAE,SAAS,MAAM,EAAE,GAAG,aAAa,CAUrE"}

package/dist/adapters/openshell-filter.js

@@ -3,7 +3,10 @@
  *
  * Implements the external content-filter contract proposed in
  * NVIDIA/OpenShell#1272 ("L7 content inspection hooks — scriptable
- * request/response filtering"): the OpenShell *supervisor* (outside the agent
+ * request/response filtering"). That proposal was closed as not planned on
+ * 2026-06-11 (OpenShell's maintainers pointed to their middleware RFC,
+ * NVIDIA/OpenShell#1733), so no OpenShell release runs this filter. The
+ * contract: the OpenShell *supervisor* (outside the agent
  * sandbox) runs this as a script against L7 request/response bodies. The body
  * arrives on stdin; the script signals the verdict via exit code:
  *
@@ -13,10 +16,14 @@
  *
  * Two run modes:
  *   one-shot (default): read the whole body from stdin, evaluate, exit.
- *       Matches the #1272 contract literally. Cold-starts the engine per call.
+ *       Matches the #1272 contract literally. Cold-starts the engine per call:
+ *       starting Node, loading the rule set and compiling its patterns take
+ *       hundreds of milliseconds to about a second.
  *   serve (--serve):    read NDJSON requests line-by-line from stdin and write
  *       one NDJSON verdict per line. Loads the rule set ONCE, so per-request
- *       latency is just regex evaluation (sub-ms). Production path for a
+ *       latency is just regex evaluation: a median of about a millisecond for
+ *       a short body, tens of milliseconds for a multi-kilobyte one
+ *       (scripts/bench-evaluate-latency.ts). Intended path for a
  *       persistent guard service (cf. NVIDIA/OpenShell#1733 RFC 0005). A bad
  *       line (or an engine error) yields a per-line error verdict and the
  *       stream continues — one malformed body cannot take the inspector offline.

package/dist/adapters/openshell-filter.js.map

@@ -1 +1 @@
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package/dist/adapters/stdio-adapter.js

@@ -75,7 +75,7 @@ export class StdioAdapter {
     async alert(ctx) {
         const alertMsg = {
             type: "alert",
-            severity: ctx.verdict.highestSeverity,
+            severity: ctx.verdict.highestSeverity ?? ctx.verdict.advisorySeverity ?? null,
             reason: ctx.verdict.reason,
             matchCount: ctx.verdict.matchCount,
         };
@@ -89,7 +89,7 @@ export class StdioAdapter {
         if (process.env.ATR_SHADOW_LOG) {
             const shadowMsg = {
                 type: "shadow",
-                severity: ctx.verdict.highestSeverity,
+                severity: ctx.verdict.highestSeverity ?? ctx.verdict.advisorySeverity ?? null,
                 reason: ctx.verdict.reason,
                 matchCount: ctx.verdict.matchCount,
                 ruleIds: ctx.matches.map((m) => m.rule.id),
@@ -116,7 +116,7 @@ export class StdioAdapter {
     async escalate(ctx) {
         const escalation = {
             type: "escalation",
-            severity: ctx.verdict.highestSeverity,
+            severity: ctx.verdict.highestSeverity ?? ctx.verdict.advisorySeverity ?? null,
             reason: ctx.verdict.reason,
             matchCount: ctx.verdict.matchCount,
         };

package/dist/adapters/stdio-adapter.js.map

@@ -1 +1 @@
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package/dist/cli/mcp-tools-document.d.ts

@@ -0,0 +1,40 @@
+/**
+ * An MCP `tools/list` document is a list of tool definitions, not an event.
+ *
+ * `atr scan tools.json` on `{"tools":[{"name":"add","description":"...","inputSchema":{...}}]}`
+ * — or on the JSON-RPC response `{"jsonrpc":"2.0","id":1,"result":{"tools":[...]}}` — used to
+ * wrap the document as one event, find no `content` on it, skip it, and report
+ * "nothing was scanned". That is the input a tool-poisoning check most often starts from.
+ *
+ * Each tool becomes its own `mcp_exchange` event:
+ *   - `content` is the tool definition as JSON, the whole object. It carries the name, the
+ *     description and the input schema, including per-parameter descriptions, extra property
+ *     fields, `required` and defaults: every one of those reaches the model, and the
+ *     full-schema-poisoning rules anchor on the schema structure (`inputSchema`, `properties`).
+ *   - `fields.tool_name` is the tool's name and `fields.tool_description` its top-level
+ *     description, for the rules that read those fields. They are set only when the definition
+ *     carries them as strings, never filled with something else.
+ * One event per tool keeps a finding attributable to a tool name.
+ *
+ * The CLI scans these events on an engine constructed with `toolDefinitions: true`, so the rules
+ * written for a tool being called do not run on them (src/tool-definition-scope.ts).
+ *
+ * @module agent-threat-rules/cli/mcp-tools-document
+ */
+import type { AgentEvent } from '../types.js';
+type JsonObject = Record<string, unknown>;
+/** One mcp_exchange event for one tool definition. */
+export declare function toolDefinitionToEvent(tool: JsonObject, timestamp: string): AgentEvent;
+/**
+ * Events for a `tools/list` document, or null when the input is not one.
+ *
+ * Accepted: `{"tools":[...]}`, `{"result":{"tools":[...]}}` (a JSON-RPC response), and a
+ * non-empty JSON array whose every element is one of those (a log of several responses).
+ * A document that lists no tools yields an empty array, so the caller reports that nothing
+ * was scanned instead of a clean result. A tools entry that is not an object yields an event
+ * with no content, which the caller counts as skipped. An object that is already an event (string
+ * content, or an event type) is never read as a tools/list document, tools array or not.
+ */
+export declare function toolsDocumentToEvents(parsed: unknown): AgentEvent[] | null;
+export {};
+//# sourceMappingURL=mcp-tools-document.d.ts.map

package/dist/cli/mcp-tools-document.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/mcp-tools-document.js

@@ -0,0 +1,95 @@
+/**
+ * An MCP `tools/list` document is a list of tool definitions, not an event.
+ *
+ * `atr scan tools.json` on `{"tools":[{"name":"add","description":"...","inputSchema":{...}}]}`
+ * — or on the JSON-RPC response `{"jsonrpc":"2.0","id":1,"result":{"tools":[...]}}` — used to
+ * wrap the document as one event, find no `content` on it, skip it, and report
+ * "nothing was scanned". That is the input a tool-poisoning check most often starts from.
+ *
+ * Each tool becomes its own `mcp_exchange` event:
+ *   - `content` is the tool definition as JSON, the whole object. It carries the name, the
+ *     description and the input schema, including per-parameter descriptions, extra property
+ *     fields, `required` and defaults: every one of those reaches the model, and the
+ *     full-schema-poisoning rules anchor on the schema structure (`inputSchema`, `properties`).
+ *   - `fields.tool_name` is the tool's name and `fields.tool_description` its top-level
+ *     description, for the rules that read those fields. They are set only when the definition
+ *     carries them as strings, never filled with something else.
+ * One event per tool keeps a finding attributable to a tool name.
+ *
+ * The CLI scans these events on an engine constructed with `toolDefinitions: true`, so the rules
+ * written for a tool being called do not run on them (src/tool-definition-scope.ts).
+ *
+ * @module agent-threat-rules/cli/mcp-tools-document
+ */
+function isObject(value) {
+    return value !== null && typeof value === 'object' && !Array.isArray(value);
+}
+/** Event types an AgentEvent carries (src/types.ts AgentEvent['type']). */
+const EVENT_TYPES = new Set([
+    'llm_input',
+    'llm_output',
+    'tool_call',
+    'tool_response',
+    'mcp_exchange',
+    'agent_behavior',
+    'multi_agent_message',
+]);
+/**
+ * An object that is already an event: string `content`, or a `type` that is an event type. Such an
+ * object stays on the event path even when it also carries a `tools` array (an LLM request logged
+ * with its tool list, for example): reading it as a tools/list document would drop its content.
+ */
+function looksLikeEvent(doc) {
+    return typeof doc['content'] === 'string' || (typeof doc['type'] === 'string' && EVENT_TYPES.has(doc['type']));
+}
+/** The tools array of a `tools/list` result, bare or inside a JSON-RPC envelope; else null. */
+function toolsArrayOf(doc) {
+    if (!isObject(doc))
+        return null;
+    if (looksLikeEvent(doc))
+        return null;
+    if (Array.isArray(doc['tools']))
+        return doc['tools'];
+    const result = doc['result'];
+    if (isObject(result) && Array.isArray(result['tools']))
+        return result['tools'];
+    return null;
+}
+/** One mcp_exchange event for one tool definition. */
+export function toolDefinitionToEvent(tool, timestamp) {
+    const name = tool['name'];
+    const description = tool['description'];
+    const fields = {
+        ...(typeof name === 'string' && name !== '' ? { tool_name: name } : {}),
+        ...(typeof description === 'string' && description !== '' ? { tool_description: description } : {}),
+    };
+    return {
+        type: 'mcp_exchange',
+        timestamp,
+        content: JSON.stringify(tool),
+        ...(Object.keys(fields).length > 0 ? { fields } : {}),
+    };
+}
+/**
+ * Events for a `tools/list` document, or null when the input is not one.
+ *
+ * Accepted: `{"tools":[...]}`, `{"result":{"tools":[...]}}` (a JSON-RPC response), and a
+ * non-empty JSON array whose every element is one of those (a log of several responses).
+ * A document that lists no tools yields an empty array, so the caller reports that nothing
+ * was scanned instead of a clean result. A tools entry that is not an object yields an event
+ * with no content, which the caller counts as skipped. An object that is already an event (string
+ * content, or an event type) is never read as a tools/list document, tools array or not.
+ */
+export function toolsDocumentToEvents(parsed) {
+    const documents = Array.isArray(parsed) ? parsed : [parsed];
+    if (documents.length === 0)
+        return null;
+    const toolLists = documents.map(toolsArrayOf);
+    if (toolLists.some((list) => list === null))
+        return null;
+    const timestamp = new Date().toISOString();
+    return toolLists.flatMap((tools) => tools.map((tool) => isObject(tool)
+        ? toolDefinitionToEvent(tool, timestamp)
+        : { type: 'mcp_exchange', timestamp, content: '' }));
+}
+//# sourceMappingURL=mcp-tools-document.js.map

package/dist/cli/mcp-tools-document.js.map

@@ -0,0 +1 @@
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package/dist/cli/scan-handler.d.ts

@@ -6,6 +6,7 @@
  */
 import type { ScanType } from '../types.js';
 import type { Lane } from '../quality/rule-contract.js';
+import { type ModelDecisions } from '../verdict.js';
 export interface ScanOptions {
     readonly rules?: string;
     readonly json?: boolean;
@@ -21,6 +22,13 @@ export interface ScanOptions {
     readonly semanticModel?: string;
     readonly semanticTimeout?: string;
     readonly semanticNoJsonMode?: boolean;
+    /**
+     * What a match a model decided (here, a semantic rule's judge) may do.
+     * 'advisory' (default): listed, marked, and not counted toward --fail-on, and
+     * written to SARIF at level note with properties.enforced false. 'enforce':
+     * counted and written like any match.
+     */
+    readonly modelDecisions?: ModelDecisions;
     /**
      * Detection lane (which rule maturities may fire). Undefined means the
      * engine's built-in default; `src/cli.ts` resolves `--lane` and `ATR_LANE`

package/dist/cli/scan-handler.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"scan-handler.d.ts","sourceRoot":"","sources":["../../src/cli/scan-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,KAAK,EAAoC,QAAQ,EAAE,MAAM,aAAa,CAAC;AAC9E,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,6BAA6B,CAAC;AAIxD,OAAO,EAAkB,KAAK,cAAc,EAAE,MAAM,eAAe,CAAC;AAoBpE,MAAM,WAAW,WAAW;IAC1B,QAAQ,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;IACxB,QAAQ,CAAC,IAAI,CAAC,EAAE,OAAO,CAAC;IACxB,QAAQ,CAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IACzB,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,SAAS,CAAC,EAAE,QAAQ,CAAC;IAC9B,QAAQ,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,aAAa,CAAC,EAAE,OAAO,CAAC;IACjC,QAAQ,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;IACxB,QAAQ,CAAC,QAAQ,CAAC,EAAE,OAAO,CAAC;IAC5B,QAAQ,CAAC,cAAc,CAAC,EAAE,MAAM,CAAC;IACjC,QAAQ,CAAC,eAAe,CAAC,EAAE,MAAM,CAAC;IAClC,QAAQ,CAAC,aAAa,CAAC,EAAE,MAAM,CAAC;IAChC,QAAQ,CAAC,eAAe,CAAC,EAAE,MAAM,CAAC;IAClC,QAAQ,CAAC,kBAAkB,CAAC,EAAE,OAAO,CAAC;IACtC;;;;;OAKG;IACH,QAAQ,CAAC,cAAc,CAAC,EAAE,cAAc,CAAC;IACzC;;;;;;OAMG;IACH,QAAQ,CAAC,IAAI,CAAC,EAAE,IAAI,CAAC;CACtB;AAED,iFAAiF;AACjF,wBAAgB,eAAe,CAAC,UAAU,EAAE,MAAM,GAAG,QAAQ,CA0B5D;AAED,6FAA6F;AAC7F,wBAAsB,cAAc,CAClC,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC,IAAI,CAAC,CA+Df"}

package/dist/cli/scan-handler.js

@@ -10,6 +10,8 @@ import { ATREngine } from '../engine.js';
 import { scanResultToSARIF } from '../converters/sarif.js';
 import { createTCReporter, resolveTcUrl } from '../tc-reporter.js';
 import { createSemanticJudgeFromConfig } from './semantic-judge-config.js';
+import { isModelDecided } from '../verdict.js';
+import { toolsDocumentToEvents } from './mcp-tools-document.js';
 const SEVERITY_ORDER = ['informational', 'low', 'medium', 'high', 'critical'];
 // ANSI colors
 const RED = '\x1b[31m';
@@ -114,6 +116,36 @@ export async function cmdScanUnified(target, rulesDir, options) {
     }
 }
 // ── MCP Event Scan ─────────────────────────────────────────────
+/**
+ * A `.mcp.json` is a configuration document, not an event.
+ *
+ * `atr scan .mcp.json` — the invocation the README shows — parsed the file, wrapped it as one
+ * event, found no `content` on it and skipped it, while the summary still said one event had been
+ * scanned. The rules never saw a single server, so a config that sets `NODE_OPTIONS` to a require
+ * payload came back as `threats_detected: 0` instead of as an error.
+ *
+ * Each server becomes its own event, with the config as its content, which is the shape the MCP
+ * rules evaluate (ATR-2026-02300, the rule written for exactly this `.mcp.json` env-block surface,
+ * fires on it — see tests/cli-mcp-config-scan.test.ts). One event per server also keeps a finding
+ * attributable to a server name.
+ */
+function configDocumentToEvents(parsed) {
+    if (!parsed || typeof parsed !== 'object' || Array.isArray(parsed))
+        return null;
+    const servers = parsed.mcpServers;
+    if (!servers || typeof servers !== 'object' || Array.isArray(servers))
+        return null;
+    const timestamp = new Date().toISOString();
+    const events = [];
+    for (const [name, config] of Object.entries(servers)) {
+        events.push({
+            type: 'mcp_exchange',
+            timestamp,
+            content: JSON.stringify({ mcpServers: { [name]: config } }),
+        });
+    }
+    return events.length > 0 ? events : null;
+}
 async function scanMcpEvents(eventsPath, rulesDir, options, reporter) {
     const fileStat = statSync(eventsPath);
     if (fileStat.size > 50 * 1024 * 1024) {
@@ -122,9 +154,18 @@ async function scanMcpEvents(eventsPath, rulesDir, options, reporter) {
     }
     const raw = readFileSync(eventsPath, 'utf-8');
     let events;
+    // Whether the input is a tools/list document: every event is then a tool definition, and the
+    // engine is told so (toolDefinitions), so the rules written for a tool being called do not run
+    // on it (src/tool-definition-scope.ts). Config documents and event files are scanned as before.
+    let toolDefinitions = false;
     try {
         const parsed = JSON.parse(raw);
-        events = Array.isArray(parsed) ? parsed : [parsed];
+        // A config document becomes one event per server, a tools/list document one event per
+        // tool; every other input is unchanged.
+        const configEvents = configDocumentToEvents(parsed);
+        const toolEvents = configEvents === null ? toolsDocumentToEvents(parsed) : null;
+        toolDefinitions = toolEvents !== null;
+        events = configEvents ?? toolEvents ?? (Array.isArray(parsed) ? parsed : [parsed]);
     }
     catch {
         console.error(`${RED}Error: Invalid JSON in ${eventsPath}${RESET}`);
@@ -136,7 +177,10 @@ async function scanMcpEvents(eventsPath, rulesDir, options, reporter) {
         reporter,
         semanticJudge: semantic.judge,
         ...(options.lane ? { lane: options.lane } : {}),
+        ...(options.modelDecisions ? { modelDecisions: options.modelDecisions } : {}),
+        ...(toolDefinitions ? { toolDefinitions: true } : {}),
     });
+    const heldBack = (m) => engine.getModelDecisions() === 'advisory' && isModelDecided(m);
     await engine.loadRules();
     if (semantic.enabled && !options.json && !options.sarif) {
         console.error(`${DIM}Semantic judge: enabled for method=semantic rules${RESET}`);
@@ -146,9 +190,14 @@ async function scanMcpEvents(eventsPath, rulesDir, options, reporter) {
     const allResults = [];
     let totalThreats = 0;
     let failHits = 0;
+    let eventsEvaluated = 0;
+    let eventsSkipped = 0;
     for (const event of events) {
-        if (!event.content)
-            continue; // skip malformed events
+        if (!event.content) {
+            eventsSkipped += 1; // skip malformed events, but never silently
+            continue;
+        }
+        eventsEvaluated += 1;
         const result = semantic.enabled
             ? await engine.evaluateFullAsync(event, eventsPath)
             : engine.evaluateFull(event, eventsPath);
@@ -157,48 +206,85 @@ async function scanMcpEvents(eventsPath, rulesDir, options, reporter) {
             allResults.push({ event, result, filtered });
             totalThreats += filtered.length;
             if (failIdx >= 0) {
-                failHits += filtered.filter((m) => SEVERITY_ORDER.indexOf(m.rule.severity) >= failIdx).length;
+                failHits += filtered.filter((m) => !heldBack(m) && SEVERITY_ORDER.indexOf(m.rule.severity) >= failIdx).length;
             }
         }
     }
+    // An event that never reached the engine is not a clean result, and the counts have to say so:
+    // `events_scanned` used to be `events.length`, computed before the skip.
+    if (events.length === 0) {
+        console.error(`${RED}Error: nothing was scanned — the input contains no events and no tools${RESET}`);
+    }
+    else if (eventsEvaluated === 0) {
+        console.error(`${RED}Error: nothing was scanned — ${eventsSkipped} event(s) had no content${RESET}`);
+    }
+    else if (eventsSkipped > 0) {
+        console.error(`${DIM}Warning: ${eventsSkipped} event(s) had no content and were not scanned${RESET}`);
+    }
+    // On a tools/list document some rules do not run (src/tool-definition-scope.ts): say so, and how
+    // many, so "not run" cannot read as "ran and found nothing"; and name the tool of each result.
+    const scope = engine.getToolDefinitionScope();
+    const scopeReport = scope
+        ? { tool_definition_scope: true, rules_evaluated: scope.rulesEvaluated, rules_skipped_by_scope: scope.rulesSkippedByScope }
+        : {};
+    const toolNameOf = (event) => toolDefinitions ? event.fields?.['tool_name'] : undefined;
     if (options.sarif) {
-        const sarifResults = allResults.map(({ result, filtered }) => ({
-            ...result,
-            matches: filtered,
-            threat_count: filtered.length,
-        }));
+        const toolNames = new Map();
+        const sarifResults = allResults.map(({ event, result, filtered }) => {
+            const scoped = { ...result, matches: filtered, threat_count: filtered.length };
+            const name = toolNameOf(event);
+            if (name !== undefined)
+                toolNames.set(scoped, name);
+            return scoped;
+        });
         const version = process.env['npm_package_version'] ?? '1.0.0';
-        console.log(JSON.stringify(scanResultToSARIF(sarifResults, version), null, 2));
-        return failHits;
+        console.log(JSON.stringify(scanResultToSARIF(sarifResults, version, {
+            heldBack,
+            ...(scope ? { runProperties: scopeReport } : {}),
+            resultProperties: (r) => (toolNames.has(r) ? { tool_name: toolNames.get(r) } : undefined),
+        }), null, 2));
+        return eventsEvaluated === 0 ? 1 : failHits;
     }
     if (options.json) {
         console.log(JSON.stringify({
             scan_type: 'mcp',
-            events_scanned: events.length,
+            events_scanned: eventsEvaluated,
+            events_skipped: eventsSkipped,
             threats_detected: totalThreats,
             rules_loaded: engine.getRuleCount(),
-            results: allResults.map(({ event, result, filtered }) => ({
-                content_hash: result.content_hash,
-                event: {
-                    type: event.type,
-                    timestamp: event.timestamp,
-                    content_preview: event.content.slice(0, 100),
-                },
-                matches: filtered.map(formatMatchJson),
-            })),
+            ...scopeReport,
+            results: allResults.map(({ event, result, filtered }) => {
+                const toolName = toolNameOf(event);
+                return {
+                    content_hash: result.content_hash,
+                    event: {
+                        type: event.type,
+                        timestamp: event.timestamp,
+                        ...(toolName !== undefined ? { tool_name: toolName } : {}),
+                        content_preview: event.content.slice(0, 100),
+                    },
+                    matches: filtered.map((m) => formatMatchJson(m, heldBack(m))),
+                };
+            }),
         }, null, 2));
-        return failHits;
+        return eventsEvaluated === 0 ? 1 : failHits;
+    }
+    printScanHeader('MCP', eventsEvaluated, engine.getRuleCount(), totalThreats);
+    if (scope) {
+        console.log(`${DIM}  Tool definitions: ${scope.rulesSkippedByScope} rule(s) written for a tool being called were not run; ${scope.rulesEvaluated} were.${RESET}\n`);
     }
-    printScanHeader('MCP', events.length, engine.getRuleCount(), totalThreats);
     if (totalThreats === 0) {
-        console.log(`${GREEN}No threats detected.${RESET}\n`);
-        return failHits;
+        console.log(eventsEvaluated === 0
+            ? `${RED}Nothing was scanned.${RESET}\n`
+            : `${GREEN}No threats detected.${RESET}\n`);
+        return eventsEvaluated === 0 ? 1 : failHits;
     }
     for (const { event, filtered } of allResults) {
         const preview = event.content.slice(0, 80).replace(/\n/g, ' ');
-        console.log(`  ${DIM}Event: [${event.type}] "${preview}..."${RESET}`);
+        const toolName = toolNameOf(event);
+        console.log(`  ${DIM}Event: [${event.type}]${toolName !== undefined ? ` tool ${toolName}` : ''} "${preview}..."${RESET}`);
         for (const m of filtered) {
-            printMatch(m);
+            printMatch(m, heldBack(m));
         }
         console.log('');
     }
@@ -217,7 +303,9 @@ async function scanSkillFiles(targetPath, rulesDir, options, reporter) {
         reporter,
         semanticJudge: semantic.judge,
         ...(options.lane ? { lane: options.lane } : {}),
+        ...(options.modelDecisions ? { modelDecisions: options.modelDecisions } : {}),
     });
+    const heldBack = (m) => engine.getModelDecisions() === 'advisory' && isModelDecided(m);
     await engine.loadRules();
     if (semantic.enabled && !options.json && !options.sarif) {
         console.error(`${DIM}Semantic judge: enabled for method=semantic rules${RESET}`);
@@ -242,7 +330,7 @@ async function scanSkillFiles(targetPath, rulesDir, options, reporter) {
             allResults.push({ file, result, filtered });
             totalThreats += filtered.length;
             if (failIdx >= 0) {
-                failHits += filtered.filter((m) => SEVERITY_ORDER.indexOf(m.rule.severity) >= failIdx).length;
+                failHits += filtered.filter((m) => !heldBack(m) && SEVERITY_ORDER.indexOf(m.rule.severity) >= failIdx).length;
             }
         }
     }
@@ -253,7 +341,7 @@ async function scanSkillFiles(targetPath, rulesDir, options, reporter) {
             threat_count: filtered.length,
         }));
         const version = process.env['npm_package_version'] ?? '1.0.0';
-        console.log(JSON.stringify(scanResultToSARIF(sarifResults, version), null, 2));
+        console.log(JSON.stringify(scanResultToSARIF(sarifResults, version, { heldBack }), null, 2));
         return failHits;
     }
     if (options.json) {
@@ -265,7 +353,7 @@ async function scanSkillFiles(targetPath, rulesDir, options, reporter) {
             results: allResults.map(({ file, result, filtered }) => ({
                 file,
                 content_hash: result.content_hash,
-                matches: filtered.map(formatMatchJson),
+                matches: filtered.map((m) => formatMatchJson(m, heldBack(m))),
             })),
         }, null, 2));
         return failHits;
@@ -279,7 +367,7 @@ async function scanSkillFiles(targetPath, rulesDir, options, reporter) {
         const relPath = file.replace(process.cwd() + '/', '');
         console.log(`  ${BOLD}${relPath}${RESET}`);
         for (const m of filtered) {
-            printMatch(m);
+            printMatch(m, heldBack(m));
         }
         console.log('');
     }
@@ -318,13 +406,16 @@ function walkForSkills(dir, out) {
         }
     }
 }
-function formatMatchJson(m) {
+function formatMatchJson(m, heldBack) {
     return {
         rule_id: m.rule.id,
         title: m.rule.title,
         severity: m.rule.severity,
         confidence: m.confidence,
         matched_conditions: m.matchedConditions,
+        decided_by: m.decidedBy ?? null,
+        // false: a model decided it and it does not count toward --fail-on.
+        enforced: !heldBack,
     };
 }
 function printScanHeader(type, scanned, rulesLoaded, threats) {
@@ -338,9 +429,10 @@ function printScanHeader(type, scanned, rulesLoaded, threats) {
     console.log(`${DIM}  Open source (MIT). Star: https://github.com/Agent-Threat-Rule/agent-threat-rules${RESET}`);
     console.log('');
 }
-function printMatch(m) {
+function printMatch(m, heldBack) {
     const color = SEVERITY_COLORS[m.rule.severity] ?? '';
-    console.log(`    ${color}${m.rule.severity.toUpperCase().padEnd(13)}${RESET} ${m.rule.id} - ${m.rule.title}`);
+    const note = heldBack ? ` ${DIM}(decided by ${m.decidedBy}: reported, not counted toward --fail-on)${RESET}` : '';
+    console.log(`    ${color}${m.rule.severity.toUpperCase().padEnd(13)}${RESET} ${m.rule.id} - ${m.rule.title}${note}`);
     console.log(`    ${DIM}Confidence: ${(m.confidence * 100).toFixed(0)}% | Conditions: ${m.matchedConditions.join(', ')}${RESET}`);
 }
 //# sourceMappingURL=scan-handler.js.map