agent-threat-rules 4.2.3 → 4.3.0

package/dist/converters/quarry.js

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+/**
+ * ATR-to-Quarry converter
+ *
+ * Exports ATR rules as Project Quarry rules (Cisco AI Defense, DSL 0.1): one
+ * `.rule` file per ATR rule, a `quarry.yaml` that loads them, and one test
+ * file per rule built from the rule's own test cases as OpenAI-shaped
+ * conversations. `check_atr_tests.py`, written next to them, runs those
+ * conversations through Quarry's scanner, so a JS/RE2 difference that a test
+ * case exercises shows up as a failing case.
+ *
+ * Field mapping (Quarry data surfaces):
+ *   user_input       -> user_messages.content, and tool_responses.content
+ *   agent_output     -> assistant_messages.content, and tool_responses.content
+ *                       (the ATR engine reads both on tool output, so
+ *                       indirect injection riding in on a tool result is seen)
+ *   tool_args        -> tool_calls.raw_arguments
+ *   tool_response    -> tool_responses.content
+ *   tool_name        -> tool_calls.name and tool_responses.name
+ *   tool_description -> tools.description
+ *   content          -> the text of user and assistant messages, tool call
+ *                       arguments and tool results. System and developer
+ *                       messages are not read: the ATR engine sees them only
+ *                       when a producer sends them as user input.
+ *
+ * What does not carry over:
+ *   - Conditions on other fields, and patterns RE2 cannot express, are
+ *     dropped. A rule whose detection is "all" loses its meaning if any
+ *     condition is dropped, so it is skipped; an "any" rule keeps the
+ *     conditions that convert. The ATR engine tests an "all" rule's
+ *     conditions on one event, so here they must hold on one item of one
+ *     surface; a rule whose conditions share no surface is skipped.
+ *   - The ATR engine folds Unicode confusables and normalizes NFKC/NFC before
+ *     matching; Quarry matches the raw text, so obfuscated input can match in
+ *     ATR and not here.
+ *   - JavaScript and RE2 differ in a few classes: JS `\s` also matches `\v`,
+ *     NBSP, the other Unicode spaces and the BOM (RE2's is ASCII only), JS `.` excludes `\r`, and a JS pattern without the
+ *     `u` flag counts an astral character as two. RE2's case folding also
+ *     maps U+017F to `s` and U+212A to `k`. The tests catch a
+ *     difference only where a test case exercises it.
+ *   - Quarry reports matches; the rules carry the ATR severity as metadata
+ *     and blocking is the application's decision.
+ *
+ * @module agent-threat-rules/converters/quarry
+ */
+import { regexConditionSpec } from '../regex-dialect.js';
+import { toRe2 } from '../re2.js';
+import { laneAllows, requiresConfirm } from '../quality/rule-contract.js';
+/** Quarry surface and item field read, per ATR field. */
+const FIELD_TARGETS = {
+    user_input: [
+        ['user_messages', 'content'],
+        ['tool_responses', 'content'],
+    ],
+    agent_output: [
+        ['assistant_messages', 'content'],
+        ['tool_responses', 'content'],
+    ],
+    tool_args: [['tool_calls', 'raw_arguments']],
+    tool_response: [['tool_responses', 'content']],
+    tool_name: [
+        ['tool_calls', 'name'],
+        ['tool_responses', 'name'],
+    ],
+    tool_description: [['tools', 'description']],
+    content: [
+        ['user_messages', 'content'],
+        ['assistant_messages', 'content'],
+        ['tool_calls', 'raw_arguments'],
+        ['tool_responses', 'content'],
+    ],
+};
+const SURFACES = ['user_messages', 'assistant_messages', 'tool_calls', 'tool_responses', 'tools'];
+/**
+ * A Quarry string literal. Quarry decodes it with Python string escapes, so
+ * every backslash is doubled and the pattern reaches RE2 unchanged.
+ */
+function quarryString(s) {
+    const escaped = s
+        .replace(/\\/g, '\\\\')
+        .replace(/"/g, '\\"')
+        .replace(/\n/g, '\\n')
+        .replace(/\r/g, '\\r')
+        .replace(/\t/g, '\\t')
+        // literal_eval rejects a raw NUL, and other control characters read better escaped.
+        .replace(/[\x00-\x1f]/g, (c) => `\\x${c.charCodeAt(0).toString(16).padStart(2, '0')}`);
+    return `"${escaped}"`;
+}
+/**
+ * A Quarry `regex` declaration. Quarry hands the text between the quotes to
+ * RE2 without decoding escapes, so escape pairs are copied as they are and
+ * only a bare quote or a line break is escaped (RE2 reads `\"`, `\n`, `\r`
+ * and `\t` as those characters).
+ */
+function quarryRegexString(pattern) {
+    let out = '';
+    for (let i = 0; i < pattern.length; i++) {
+        const ch = pattern[i];
+        if (ch === '\\' && i + 1 < pattern.length) {
+            // A backslash before a line break is an identity escape in JS; RE2 reads `\n` the same way.
+            const next = pattern[i + 1];
+            out += next === '\n' ? '\\n' : next === '\r' ? '\\r' : next === '\t' ? '\\t' : ch + next;
+            i++;
+        }
+        else if (ch === '"')
+            out += '\\"';
+        else if (ch === '\n')
+            out += '\\n';
+        else if (ch === '\r')
+            out += '\\r';
+        else if (ch === '\t')
+            out += '\\t';
+        else
+            out += ch;
+    }
+    return `"${out}"`;
+}
+/** One ATR regex condition, or null when it cannot be converted. */
+function convertCondition(cond) {
+    const targets = FIELD_TARGETS[cond.field];
+    if (!targets || cond.operator !== 'regex' || !cond.value)
+        return null;
+    const spec = regexConditionSpec(cond.value);
+    const re2 = toRe2(spec.source);
+    if (re2 === null)
+        return null;
+    try {
+        return { re2, targets, js: new RegExp(spec.source, spec.flags) };
+    }
+    catch {
+        return null; // the ATR engine cannot compile it either
+    }
+}
+const fieldOn = (c, surface) => c.targets.find(([s]) => s === surface)?.[1];
+/** Surfaces on which every condition reads a field. */
+function sharedSurfaces(conditions) {
+    return SURFACES.filter((s) => conditions.every((c) => fieldOn(c, s) !== undefined));
+}
+/**
+ * The rule's `condition:` expression, one comprehension per surface (Quarry
+ * warns on rules with many). Condition i is declared as `$p<i>`.
+ */
+function conditionExpression(conditions, logic) {
+    const surfaces = logic === 'all' ? sharedSurfaces(conditions) : SURFACES;
+    const clauses = surfaces.flatMap((s) => {
+        const tests = conditions.flatMap((c, i) => {
+            const field = fieldOn(c, s);
+            return field === undefined ? [] : [`($p${i} in x.${field})`];
+        });
+        if (tests.length === 0)
+            return [];
+        const body = tests.length === 1 ? tests[0] : `(${tests.join(logic === 'all' ? ' and ' : ' or ')})`;
+        return [`(any x in ${s} where ${body})`];
+    });
+    return clauses.join('\n    or ');
+}
+const CALL_ID = 'call_atr_1';
+const DEFAULT_TOOL = 'atr_test_tool';
+/**
+ * Where a plain-text test case goes. ATR's `input` key is the text of
+ * whatever the rule reads, so a rule that reads only tool output gets a tool
+ * result, and one that reads only tool arguments gets a tool call.
+ */
+function plainTextKey(fields) {
+    // A named field says where the text belongs; `content` alone does not.
+    for (const f of ['tool_response', 'tool_args', 'user_input', 'agent_output', 'tool_description']) {
+        if (fields.has(f))
+            return f;
+    }
+    return 'user_input';
+}
+/**
+ * Tool-call argument text Quarry accepts: the text itself when it is a JSON
+ * object, else `{"input": <text>}`. The wrapped text is JSON-escaped, so a
+ * pattern that relies on a quote, backslash or control character in it can
+ * miss; the coverage check then reports that true positive.
+ */
+function asJsonObjectText(text) {
+    try {
+        const parsed = JSON.parse(text);
+        if (parsed !== null && typeof parsed === 'object' && !Array.isArray(parsed))
+            return text;
+    }
+    catch {
+        // not JSON
+    }
+    return JSON.stringify({ input: text });
+}
+/** The conversation for one ATR test case, or null when the case has no mappable field. */
+function testConversation(tc, fields) {
+    const str = (v) => (typeof v === 'string' ? v : JSON.stringify(v));
+    const parts = {};
+    for (const key of ['user_input', 'agent_output', 'tool_args', 'tool_response', 'tool_description']) {
+        if (tc[key] !== undefined && tc[key] !== null)
+            parts[key] = str(tc[key]);
+    }
+    const plain = tc['input'] ?? tc['content'];
+    if (typeof plain === 'string') {
+        const key = plainTextKey(fields);
+        parts[key] ??= plain;
+    }
+    const name = typeof tc['tool_name'] === 'string' && tc['tool_name'] ? tc['tool_name'] : undefined;
+    if (Object.keys(parts).length === 0 && name === undefined)
+        return null;
+    const tool = name ?? DEFAULT_TOOL;
+    const messages = [];
+    if (parts['user_input'] !== undefined)
+        messages.push({ role: 'user', content: parts['user_input'] });
+    // Quarry requires tool-call arguments to be a JSON object, so other text is wrapped as one.
+    const args = parts['tool_args'] === undefined ? undefined : asJsonObjectText(parts['tool_args']);
+    const calls = parts['tool_args'] !== undefined || parts['tool_response'] !== undefined || name !== undefined;
+    if (calls) {
+        messages.push({
+            role: 'assistant',
+            content: null,
+            tool_calls: [{ id: CALL_ID, type: 'function', function: { name: tool, arguments: args ?? '{}' } }],
+        });
+        if (parts['tool_response'] !== undefined)
+            messages.push({ role: 'tool', tool_call_id: CALL_ID, content: parts['tool_response'] });
+    }
+    if (parts['agent_output'] !== undefined)
+        messages.push({ role: 'assistant', content: parts['agent_output'] });
+    const description = parts['tool_description'];
+    if (messages.length === 0)
+        messages.push({ role: 'user', content: '' });
+    return description === undefined
+        ? { messages }
+        : { messages, tools: [{ type: 'function', function: { name: tool, description, parameters: { type: 'object', properties: {} } } }] };
+}
+/** The items of each surface in a conversation, as Quarry exposes them. */
+function surfaceItems(conv) {
+    const items = {
+        user_messages: [],
+        assistant_messages: [],
+        tool_calls: [],
+        tool_responses: [],
+        tools: [],
+    };
+    const callNames = new Map();
+    for (const m of conv.messages) {
+        if (m.role === 'user')
+            items.user_messages.push({ content: m.content });
+        if (m.role === 'assistant') {
+            items.assistant_messages.push({ content: m.content ?? '' });
+            for (const call of m.tool_calls ?? []) {
+                callNames.set(call.id, call.function.name);
+                items.tool_calls.push({ name: call.function.name, raw_arguments: call.function.arguments });
+            }
+        }
+        if (m.role === 'tool')
+            items.tool_responses.push({ content: m.content, name: callNames.get(m.tool_call_id) ?? '' });
+    }
+    for (const t of conv.tools ?? [])
+        items.tools.push({ name: t.function.name, description: t.function.description });
+    return items;
+}
+/** Does the converted rule match this conversation, judged with the JS patterns? */
+function ruleMatches(conditions, logic, conv) {
+    const items = surfaceItems(conv);
+    const hit = (c, item, field) => {
+        const value = item[field];
+        c.js.lastIndex = 0;
+        return typeof value === 'string' && c.js.test(value);
+    };
+    if (logic === 'all') {
+        return sharedSurfaces(conditions).some((s) => items[s].some((item) => conditions.every((c) => hit(c, item, fieldOn(c, s)))));
+    }
+    return conditions.some((c) => c.targets.some(([s, f]) => items[s].some((item) => hit(c, item, f))));
+}
+/**
+ * The rule's test conversations. A true positive that only a dropped
+ * condition caught would fail in Quarry, so it is left out and reported.
+ */
+function buildTests(rule, converted, logic) {
+    const fields = new Set(arrayConditions(rule)?.map((c) => c.field) ?? []);
+    const cases = [];
+    const uncovered = [];
+    const unmapped = [];
+    const add = (list, expect, label) => {
+        if (!Array.isArray(list))
+            return;
+        list.forEach((tc, i) => {
+            const conversation = tc && typeof tc === 'object' ? testConversation(tc, fields) : null;
+            if (!conversation) {
+                unmapped.push(`${expect === 'match' ? 'tp' : 'tn'}-${i + 1}`);
+                return;
+            }
+            if (expect === 'match' && !ruleMatches(converted, logic, conversation)) {
+                uncovered.push(i + 1);
+                return;
+            }
+            cases.push({ name: `${label}-${i + 1}`, expect, conversation });
+        });
+    };
+    add(rule.test_cases?.true_positives, 'match', 'atr-true-positive');
+    add(rule.test_cases?.true_negatives, 'no_match', 'atr-true-negative');
+    return { cases, uncovered, unmapped };
+}
+function arrayConditions(rule) {
+    return Array.isArray(rule.detection.conditions) ? rule.detection.conditions : null;
+}
+/** Convert one ATR rule, or say why it cannot be converted. */
+export function ruleToQuarry(rule) {
+    const conditions = arrayConditions(rule);
+    if (!conditions)
+        return { ruleId: rule.id, reason: 'named-format conditions are not supported' };
+    const converted = [];
+    const dropped = [];
+    conditions.forEach((cond, i) => {
+        const c = convertCondition(cond);
+        if (c === null)
+            dropped.push(i);
+        else
+            converted.push(c);
+    });
+    const logic = String(rule.detection.condition ?? 'any').trim().toLowerCase();
+    if (logic !== 'any' && logic !== 'all')
+        return { ruleId: rule.id, reason: `detection condition "${logic}" is not supported` };
+    if (converted.length === 0)
+        return { ruleId: rule.id, reason: 'no condition converts (fields or RE2)' };
+    if (logic === 'all' && dropped.length > 0) {
+        return { ruleId: rule.id, reason: 'an "all" rule with an unconvertible condition would change meaning' };
+    }
+    if (logic === 'all' && sharedSurfaces(converted).length === 0) {
+        return { ruleId: rule.id, reason: 'an "all" rule whose conditions read different Quarry surfaces can never match' };
+    }
+    if (!/^ATR-\d{4}-\d{5}$/.test(rule.id))
+        return { ruleId: rule.id, reason: 'rule id is not in ATR-YYYY-NNNNN form' };
+    const metadata = [
+        ['title', rule.title],
+        ['severity', rule.severity],
+        ['category', String(rule.tags.category)],
+        ['maturity', String(rule.maturity ?? '')],
+        ['rule_version', String(rule.rule_version ?? 1)],
+        ['source', `Agent Threat Rules ${rule.id} (https://github.com/Agent-Threat-Rule/agent-threat-rules)`],
+    ];
+    const text = [
+        `rule ${quarryString(rule.id)}`,
+        'metadata:',
+        ...metadata.map(([k, v]) => `    ${k} = ${quarryString(v)}`),
+        'strings:',
+        // SPEC §6.4: every condition matches case-insensitively.
+        ...converted.map((c, i) => `    $p${i} = ${quarryRegexString(c.re2)} regex nocase`),
+        'condition:',
+        `    ${conditionExpression(converted, logic)}`,
+        '',
+    ].join('\n');
+    const tests = buildTests(rule, converted, logic);
+    return {
+        ruleId: rule.id,
+        stem: rule.id.toLowerCase(),
+        rule: text,
+        tests: tests.cases,
+        droppedConditions: dropped,
+        uncoveredTruePositives: tests.uncovered,
+        unmappedCases: tests.unmapped,
+    };
+}
+/** Convert the rules in `lane` (default `enforce`). Embedding-confirmed rules are left out of enforce and alert. */
+export function rulesToQuarry(rules, options = {}) {
+    const lane = options.lane ?? 'enforce';
+    const files = [];
+    const skipped = [];
+    for (const rule of rules) {
+        if (rule.status === 'draft' || rule.status === 'deprecated')
+            continue;
+        if (!laneAllows(rule.maturity, lane))
+            continue;
+        if (lane !== 'hunt' && requiresConfirm(rule)) {
+            skipped.push({ ruleId: rule.id, reason: 'needs embedding confirmation, which this export does not run' });
+            continue;
+        }
+        const out = ruleToQuarry(rule);
+        if ('reason' in out)
+            skipped.push(out);
+        else
+            files.push(out);
+    }
+    return { files, skipped };
+}
+/** `quarry.yaml`, loading the exported rules. Quarry resolves `rules/` against the working directory. */
+export const QUARRY_CONFIG = 'config_version: 2\nrules:\n  - rules/\n';
+/** `check_atr_tests.py`: runs each rule's ATR test conversations through Quarry. */
+export const QUARRY_CHECK_SCRIPT = `"""Run the ATR test cases exported with these rules through Quarry.
+
+With Quarry installed:
+
+    python check_atr_tests.py
+
+Each tests/<rule>.json holds that rule's ATR true positives (expect "match")
+and true negatives (expect "no_match") as conversations. A case passes when
+the named rule's verdict is what the case expects; other rules may match too.
+Exits 1 if any case fails or any scan is incomplete.
+"""
+
+import json
+import os
+import sys
+from pathlib import Path
+
+from quarry import DSLScanner
+from quarry.config import QuarryConfig
+
+HERE = Path(__file__).resolve().parent
+
+
+def main() -> int:
+    # Quarry resolves the rules path in quarry.yaml against the working directory.
+    os.chdir(HERE)
+    scanner = DSLScanner(QuarryConfig.from_yaml(HERE / "quarry.yaml"))
+    total = failed = 0
+    for path in sorted((HERE / "tests").glob("*.json")):
+        suite = json.loads(path.read_text(encoding="utf-8"))
+        for case in suite["cases"]:
+            total += 1
+            result = scanner.scan_data(case["conversation"])
+            if not result.is_complete:
+                failed += 1
+                print(f"{suite['rule']} {case['name']}: scan {result.completion_state}")
+                continue
+            matched = suite["rule"] in result.rule_matches
+            if matched != (case["expect"] == "match"):
+                failed += 1
+                print(f"{suite['rule']} {case['name']}: expected {case['expect']}")
+    print(f"{total - failed}/{total} cases pass")
+    return 1 if failed else 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())
+`;
+//# sourceMappingURL=quarry.js.map

package/dist/converters/quarry.js.map

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package/dist/converters/sarif.d.ts

@@ -25,6 +25,13 @@ export interface SarifOptions {
     readonly runProperties?: Readonly<Record<string, unknown>>;
     /** Extra properties for every result of one scan result (e.g. the tool name of a tools/list entry). */
     readonly resultProperties?: (result: ScanResult) => Readonly<Record<string, unknown>> | undefined;
+    /** Files the tool deliberately skipped, reported as SARIF execution warnings. */
+    readonly skippedFiles?: readonly {
+        readonly file: string;
+        readonly reason: string;
+    }[];
+    /** Whether the invocation produced at least one scan result. */
+    readonly executionSuccessful?: boolean;
 }
 export declare function scanResultToSARIF(results: readonly ScanResult[], toolVersion: string, options?: SarifOptions): object;
 //# sourceMappingURL=sarif.d.ts.map

package/dist/converters/sarif.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sarif.d.ts","sourceRoot":"","sources":["../../src/converters/sarif.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,KAAK,EAAW,QAAQ,EAAE,UAAU,EAAe,MAAM,aAAa,CAAC;AAkG9E;;;;;;GAMG;AACH,MAAM,WAAW,YAAY;IAC3B;;;;OAIG;IACH,QAAQ,CAAC,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,QAAQ,KAAK,OAAO,CAAC;IACjD,6GAA6G;IAC7G,QAAQ,CAAC,aAAa,CAAC,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;IAC3D,uGAAuG;IACvG,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC,MAAM,EAAE,UAAU,KAAK,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GAAG,SAAS,CAAC;CACnG;AAED,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,SAAS,UAAU,EAAE,EAC9B,WAAW,EAAE,MAAM,EACnB,OAAO,GAAE,YAAiB,GACzB,MAAM,CAgHR"}
+{"version":3,"file":"sarif.d.ts","sourceRoot":"","sources":["../../src/converters/sarif.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,KAAK,EAAW,QAAQ,EAAE,UAAU,EAAe,MAAM,aAAa,CAAC;AAuG9E;;;;;;GAMG;AACH,MAAM,WAAW,YAAY;IAC3B;;;;OAIG;IACH,QAAQ,CAAC,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,QAAQ,KAAK,OAAO,CAAC;IACjD,6GAA6G;IAC7G,QAAQ,CAAC,aAAa,CAAC,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;IAC3D,uGAAuG;IACvG,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC,MAAM,EAAE,UAAU,KAAK,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GAAG,SAAS,CAAC;IAClG,iFAAiF;IACjF,QAAQ,CAAC,YAAY,CAAC,EAAE,SAAS;QAAE,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAA;KAAE,EAAE,CAAC;IACtF,gEAAgE;IAChE,QAAQ,CAAC,mBAAmB,CAAC,EAAE,OAAO,CAAC;CACxC;AAED,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,SAAS,UAAU,EAAE,EAC9B,WAAW,EAAE,MAAM,EACnB,OAAO,GAAE,YAAiB,GACzB,MAAM,CAqIR"}

package/dist/converters/sarif.js

@@ -71,6 +71,10 @@ function toArtifactUri(inputFile) {
     }
     return inputFile;
 }
+/** Keep filesystem diagnostics useful without publishing the scanner's absolute path. */
+function skippedReasonForSarif(reason, file, uri) {
+    return file === uri ? reason : reason.split(file).join(uri);
+}
 /**
  * Raw-octet SHA-256 of a file's bytes — the digest basis the shared envelope
  * profile joins layers on (claude-code-skill-security-check#24 §2): computed
@@ -181,6 +185,20 @@ export function scanResultToSARIF(results, toolVersion, options = {}) {
             });
         }
     }
+    const toolExecutionNotifications = options.skippedFiles?.map(({ file, reason }) => {
+        const uri = toArtifactUri(file);
+        const safeReason = skippedReasonForSarif(reason, file, uri);
+        return {
+            descriptor: { id: 'ATR_SCAN_SKIPPED' },
+            level: 'warning',
+            message: { text: `Skipped ${uri}: ${safeReason}` },
+            locations: [{
+                    physicalLocation: {
+                        artifactLocation: { uri, uriBaseId: '%SRCROOT%' },
+                    },
+                }],
+        };
+    }) ?? [];
     return {
         $schema: 'https://raw.githubusercontent.com/oasis-tcs/sarif-spec/main/sarif-2.1/schema/sarif-schema-2.1.0.json',
         version: '2.1.0',
@@ -196,6 +214,12 @@ export function scanResultToSARIF(results, toolVersion, options = {}) {
                     },
                 },
                 ...(artifacts.length > 0 ? { artifacts } : {}),
+                ...(toolExecutionNotifications.length > 0 ? {
+                    invocations: [{
+                            executionSuccessful: options.executionSuccessful ?? true,
+                            toolExecutionNotifications,
+                        }],
+                } : {}),
                 ...(options.runProperties ? { properties: options.runProperties } : {}),
                 results: sarifResults,
             },

package/dist/converters/sarif.js.map

@@ -1 +1 @@
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package/dist/engine.d.ts.map

@@ -1 +1 @@
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package/dist/engine.js

@@ -301,7 +301,13 @@ export class ATREngine {
         const rulesDir = this.config.rulesDir ?? this.findBundledRulesDir();
         if (rulesDir) {
             try {
-                const fileRules = loadRulesFromDirectory(rulesDir);
+                // A rule passed in config overrides the directory's rule with that id.
+                // Compiled patterns are keyed by id, so keeping both ran the directory
+                // copy's regex under the passed rule's name. Duplicates inside the
+                // directory are left in place for the id-collision and measurement
+                // gates to see.
+                const passed = new Set((this.config.rules ?? []).map((r) => r.id));
+                const fileRules = loadRulesFromDirectory(rulesDir).filter((r) => !passed.has(r.id));
                 this.rules.push(...fileRules);
             }
             catch {