circle-ir-ai 2.32.0 → 2.33.2

package/dist/cache/cluster-cache.d.ts

@@ -0,0 +1,113 @@
+/**
+ * Cluster Cache
+ *
+ * Persistent on-disk cache for `clusterFiles()` output (cognium-ai#154,
+ * P4 of epic #155 wiring — Sprint L5c).
+ *
+ * K-medoids assignments are a pure function of:
+ *   - the set of file paths in the scan
+ *   - each file's CK vector + imports + annotations (structural
+ *     fingerprint from `extractClusterVector`)
+ *   - the algorithm version sentinel `PROMPT_VER = 'cluster-v1'`
+ *   - the rule-set fingerprint + normalized project profile
+ *     (rules/profile don't affect the clustering *result*, but do
+ *     affect downstream policy application, so we key on them anyway
+ *     for cross-runner replay safety)
+ *
+ * Caching this eliminates the O(n²) distance-matrix pass + k-medoids
+ * swap phase on warm re-scans of the same repo, which is the hot path
+ * during iterative development.
+ *
+ * **Scope:** caches whole-repo `ClusterResult` only. Never per-file.
+ *
+ * **Key composition:**
+ *
+ *   content    = ckVectorSig + '\0' + circleIrVersion + '\0' +
+ *                circleIrAiVersion + '\0' + ruleSetFingerprint + '\0' +
+ *                PROMPT_VER + '\0' + k
+ *   classifier = 'cluster-kmedoids'
+ *
+ * `ckVectorSig` folds the sorted (filePath, vector-signature) pairs —
+ * matches the shape `deriveSeed()` uses in cluster.ts:316-326 so the
+ * cache key changes exactly when the cluster assignments would.
+ *
+ * Any of: file add/remove, file structural edit, circle-ir bump,
+ * circle-ir-ai bump, rule-set change, k change, PROMPT_VER bump →
+ * cache miss.
+ *
+ * **Env toggles:**
+ *   LLM_CLUSTER_CACHE=0  → disable persistent cluster cache.
+ */
+import { ClassificationCache } from './classification-cache.js';
+import type { ClusterInput, ClusterResult } from '../cluster/cluster.js';
+/**
+ * On-disk envelope. Mirrors `ClusterResult` from cluster.ts but adds a
+ * schema tag + captured versions so a future format change is
+ * self-describing at read time. Kept separate from `ClusterResult`
+ * itself so downstream consumers of the runtime API don't drag the
+ * cache envelope into their surface.
+ */
+export interface ClusterCacheEntry {
+    schema: 'cluster:v1';
+    k: number;
+    assignments: Array<{
+        filePath: string;
+        clusterId: number;
+    }>;
+    medoids: string[];
+    iterations: number;
+    /** SHA256 of the input CK-vector signature (for debugging cache hits). */
+    ckVectorSig: string;
+    /** Wall-clock timestamp at write. Diagnostic only; TTL comes from ClassificationCache. */
+    computedAt: number;
+}
+/**
+ * Get the cluster-cache singleton. When `LLM_CLUSTER_CACHE=0` returns
+ * a disabled cache that no-ops on get/set.
+ */
+export declare function getClusterCache(): ClassificationCache<ClusterCacheEntry>;
+/** Reset the module-scoped singleton — test-only. */
+export declare function resetClusterCache(): void;
+/**
+ * Fold the sorted (filePath, per-file vector signature) pairs into a
+ * single stable string. Mirrors the shape used by `deriveSeed()` in
+ * cluster.ts:316-326 so the cache key changes exactly when the cluster
+ * result would.
+ */
+export declare function ckVectorSignature(inputs: ClusterInput[]): string;
+/**
+ * Compute the `(content, classifier)` tuple for the underlying
+ * ClassificationCache. `ruleSetFingerprint` is threaded through so
+ * two runners on the same repo but different rule sets don't share
+ * (they'd apply different policies downstream even on identical
+ * cluster assignments).
+ */
+export declare function computeClusterCacheKey(input: {
+    inputs: ClusterInput[];
+    k: number;
+    ruleSetFingerprint?: string;
+}): {
+    content: string;
+    classifier: string;
+    ckVectorSig: string;
+};
+/** Test-only: expose the captured engine versions for assertions. */
+export declare function getClusterCacheVersions(): {
+    circleIrVersion: string;
+    circleIrAiVersion: string;
+};
+/** Test-only: expose the prompt-version sentinel. */
+export declare function getClusterCachePromptVersion(): string;
+/**
+ * Convert a runtime `ClusterResult` into the persisted envelope shape.
+ * Split out so the scanner call site doesn't have to know about the
+ * envelope; test suite uses it as a factory too.
+ */
+export declare function toCacheEntry(result: ClusterResult, ckVectorSig: string): ClusterCacheEntry;
+/**
+ * Rehydrate a `ClusterResult` from a persisted envelope. Envelope
+ * shape validation is best-effort — a mismatched schema returns null
+ * so the caller treats it as a miss and recomputes.
+ */
+export declare function fromCacheEntry(entry: ClusterCacheEntry): ClusterResult | null;
+//# sourceMappingURL=cluster-cache.d.ts.map

package/dist/cache/cluster-cache.d.ts.map

@@ -0,0 +1 @@
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package/dist/cache/cluster-cache.js

@@ -0,0 +1,195 @@
+/**
+ * Cluster Cache
+ *
+ * Persistent on-disk cache for `clusterFiles()` output (cognium-ai#154,
+ * P4 of epic #155 wiring — Sprint L5c).
+ *
+ * K-medoids assignments are a pure function of:
+ *   - the set of file paths in the scan
+ *   - each file's CK vector + imports + annotations (structural
+ *     fingerprint from `extractClusterVector`)
+ *   - the algorithm version sentinel `PROMPT_VER = 'cluster-v1'`
+ *   - the rule-set fingerprint + normalized project profile
+ *     (rules/profile don't affect the clustering *result*, but do
+ *     affect downstream policy application, so we key on them anyway
+ *     for cross-runner replay safety)
+ *
+ * Caching this eliminates the O(n²) distance-matrix pass + k-medoids
+ * swap phase on warm re-scans of the same repo, which is the hot path
+ * during iterative development.
+ *
+ * **Scope:** caches whole-repo `ClusterResult` only. Never per-file.
+ *
+ * **Key composition:**
+ *
+ *   content    = ckVectorSig + '\0' + circleIrVersion + '\0' +
+ *                circleIrAiVersion + '\0' + ruleSetFingerprint + '\0' +
+ *                PROMPT_VER + '\0' + k
+ *   classifier = 'cluster-kmedoids'
+ *
+ * `ckVectorSig` folds the sorted (filePath, vector-signature) pairs —
+ * matches the shape `deriveSeed()` uses in cluster.ts:316-326 so the
+ * cache key changes exactly when the cluster assignments would.
+ *
+ * Any of: file add/remove, file structural edit, circle-ir bump,
+ * circle-ir-ai bump, rule-set change, k change, PROMPT_VER bump →
+ * cache miss.
+ *
+ * **Env toggles:**
+ *   LLM_CLUSTER_CACHE=0  → disable persistent cluster cache.
+ */
+import * as crypto from 'crypto';
+import * as fs from 'fs';
+import * as path from 'path';
+import { createRequire } from 'module';
+import { ClassificationCache } from './classification-cache.js';
+const CLUSTER_CACHE_SUBDIR = path.join('.cognium', 'cache');
+const CLUSTER_CACHE_TTL_MS = 7 * 24 * 60 * 60 * 1000; // 7 days — structural, stable
+/**
+ * Algorithm-version sentinel. Bump on any change to k-selection,
+ * distance weights, seed derivation, or the swap-phase loop in
+ * `cluster.ts`. Keeps the key composition structurally identical to
+ * the three LLM caches (tree/verify/discovery) even though clustering
+ * doesn't call an LLM — the sentinel gives us a single dial to
+ * invalidate all cluster entries if the algorithm ever changes.
+ */
+const PROMPT_VER = 'cluster-v1';
+let _instance = null;
+function safeReadVersion(spec, baseUrl) {
+    try {
+        const require = createRequire(baseUrl);
+        return require(spec).version || 'unknown';
+    }
+    catch {
+        return 'unknown';
+    }
+}
+const _circleIrVersion = safeReadVersion('circle-ir/package.json', import.meta.url);
+const _circleIrAiVersion = (() => {
+    try {
+        const candidates = [
+            path.resolve(new URL(import.meta.url).pathname, '../../../package.json'),
+            path.resolve(new URL(import.meta.url).pathname, '../../package.json'),
+        ];
+        for (const p of candidates) {
+            if (fs.existsSync(p)) {
+                const pkg = JSON.parse(fs.readFileSync(p, 'utf8'));
+                if (pkg.name === 'circle-ir-ai' && pkg.version) {
+                    return pkg.version;
+                }
+            }
+        }
+    }
+    catch {
+        /* fallthrough */
+    }
+    return 'unknown';
+})();
+/**
+ * Get the cluster-cache singleton. When `LLM_CLUSTER_CACHE=0` returns
+ * a disabled cache that no-ops on get/set.
+ */
+export function getClusterCache() {
+    const enabled = process.env.LLM_CLUSTER_CACHE !== '0';
+    if (!_instance) {
+        _instance = new ClassificationCache({
+            namespace: 'cluster',
+            cacheDir: path.join(process.cwd(), CLUSTER_CACHE_SUBDIR),
+            maxAge: CLUSTER_CACHE_TTL_MS,
+            enabled,
+            // modelFingerprint deliberately omitted — clustering is static.
+        });
+    }
+    return _instance;
+}
+/** Reset the module-scoped singleton — test-only. */
+export function resetClusterCache() {
+    _instance = null;
+}
+/**
+ * Fold the sorted (filePath, per-file vector signature) pairs into a
+ * single stable string. Mirrors the shape used by `deriveSeed()` in
+ * cluster.ts:316-326 so the cache key changes exactly when the cluster
+ * result would.
+ */
+export function ckVectorSignature(inputs) {
+    const sig = inputs
+        .map((i) => `${i.filePath}\0${i.vector.cbo},${i.vector.rfc},${i.vector.lcom},${i.vector.dit},${i.vector.noc},${i.vector.wmc},${i.vector.publicSurface}\0${[...i.vector.imports].sort().join(',')}\0${[...i.vector.annotations].sort().join(',')}`)
+        .sort()
+        .join('|');
+    return crypto.createHash('sha256').update(sig).digest('hex');
+}
+/**
+ * Compute the `(content, classifier)` tuple for the underlying
+ * ClassificationCache. `ruleSetFingerprint` is threaded through so
+ * two runners on the same repo but different rule sets don't share
+ * (they'd apply different policies downstream even on identical
+ * cluster assignments).
+ */
+export function computeClusterCacheKey(input) {
+    const ckVectorSig = ckVectorSignature(input.inputs);
+    const ruleSet = input.ruleSetFingerprint ?? '';
+    return {
+        content: [
+            ckVectorSig,
+            _circleIrVersion,
+            _circleIrAiVersion,
+            ruleSet,
+            PROMPT_VER,
+            String(input.k),
+        ].join('\0'),
+        classifier: 'cluster-kmedoids',
+        ckVectorSig,
+    };
+}
+/** Test-only: expose the captured engine versions for assertions. */
+export function getClusterCacheVersions() {
+    return {
+        circleIrVersion: _circleIrVersion,
+        circleIrAiVersion: _circleIrAiVersion,
+    };
+}
+/** Test-only: expose the prompt-version sentinel. */
+export function getClusterCachePromptVersion() {
+    return PROMPT_VER;
+}
+/**
+ * Convert a runtime `ClusterResult` into the persisted envelope shape.
+ * Split out so the scanner call site doesn't have to know about the
+ * envelope; test suite uses it as a factory too.
+ */
+export function toCacheEntry(result, ckVectorSig) {
+    return {
+        schema: 'cluster:v1',
+        k: result.k,
+        assignments: result.assignments.map((a) => ({
+            filePath: a.filePath,
+            clusterId: a.clusterId,
+        })),
+        medoids: [...result.medoids],
+        iterations: result.iterations,
+        ckVectorSig,
+        computedAt: Date.now(),
+    };
+}
+/**
+ * Rehydrate a `ClusterResult` from a persisted envelope. Envelope
+ * shape validation is best-effort — a mismatched schema returns null
+ * so the caller treats it as a miss and recomputes.
+ */
+export function fromCacheEntry(entry) {
+    if (entry.schema !== 'cluster:v1')
+        return null;
+    if (!Array.isArray(entry.assignments) || !Array.isArray(entry.medoids))
+        return null;
+    return {
+        k: entry.k,
+        assignments: entry.assignments.map((a) => ({
+            filePath: a.filePath,
+            clusterId: a.clusterId,
+        })),
+        medoids: entry.medoids,
+        iterations: entry.iterations,
+    };
+}
+//# sourceMappingURL=cluster-cache.js.map

package/dist/cache/cluster-cache.js.map

@@ -0,0 +1 @@
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package/dist/cache/tree-cache.d.ts

@@ -38,6 +38,7 @@
  */
 import { ClassificationCache } from './classification-cache.js';
 import type { TaintSource, TaintSink, TypeInfo, DFG, SastFinding } from 'circle-ir';
+import type { ClusterVector } from '../cluster/cluster.js';
 /**
  * Shape persisted to disk. Mirrors the return of `runPatternMatch` in
  * `src/agents/mastra/workflow.ts`. All fields are plain JSON-serializable.
@@ -49,6 +50,16 @@ export interface PatternMatchResult {
     imports: string[];
     sastFindings: SastFinding[];
     dfg: DFG;
+    /**
+     * cognium-ai#154 (L5c) — CK + import/annotation fingerprint used by
+     * the top-level cluster pass. Extracted from `CircleIR` inside
+     * `runPatternMatch` while the IR is live so downstream cluster
+     * wiring doesn't need to re-invoke `analyze()`. Optional so older
+     * cached entries (written before 2.33.0) deserialize cleanly — the
+     * scanner treats an absent vector as "skip this file from
+     * clustering" rather than as a hard error.
+     */
+    clusterVector?: ClusterVector;
 }
 /**
  * Get the tree-cache singleton. When `LLM_TREE_CACHE=0` returns a

package/dist/cache/tree-cache.d.ts.map

@@ -1 +1 @@
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package/dist/cache/tree-cache.js.map

@@ -1 +1 @@
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package/dist/security-scan/scanner.d.ts

@@ -8,6 +8,7 @@
  * - Trend tracking (store results, compare across runs)
  */
 import { type Finding, type ProjectProfile, type SupportedLanguage } from 'circle-ir';
+import { type ClusterPolicy, type ClusterResult, type ClusterVector, type ContextProfile } from '../cluster/cluster.js';
 import { type OWASPMapping } from './owasp-mapping.js';
 import { type ParseFailure } from './parse-failure.js';
 export type { ParseFailure, ParseFailureReason } from './parse-failure.js';
@@ -75,6 +76,37 @@ export interface ScanOptions {
      * preserved on each `SastFinding`). C-Yes-Yes policy per ADR-008.
      */
     projectProfile?: ProjectProfile | Map<string, ProjectProfile>;
+    /**
+     * cognium-ai#154 (L5c) — per-cluster policy overrides. When provided,
+     * `applyClusterPolicies()` filters each `FileResult`'s findings using
+     * the policy assigned to that file's cluster (by `FileResult.clusterId`).
+     *
+     * Interaction with `contextProfile`:
+     *   - `clusterPolicies` set → per-cluster policy takes precedence for
+     *     any cluster id present in the map;
+     *   - `contextProfile` set → applied uniformly to every cluster whose
+     *     id is NOT covered by `clusterPolicies`;
+     *   - neither set → `DEFAULT_CLUSTER_POLICY` applied uniformly (byte-
+     *     identical to pre-2.33.0 behavior, no filter fires).
+     *
+     * Absent-`clusterId` files (parse failures, pre-flight skips) are
+     * never filtered — the policy layer only sees files that made it
+     * through `runClusterPass()`.
+     */
+    clusterPolicies?: Map<number, ClusterPolicy>;
+    /**
+     * cognium-ai#154 (L5c) — uniform cluster policy resolved from the
+     * cognium-ai `--cluster-policy <profile>` CLI flag. Applied to every
+     * cluster whose id is not overridden by `clusterPolicies`. Also
+     * echoed into `ScanMeta.contextProfile` for downstream observability
+     * (top-100 sweep operating principles P2: track which profile fired
+     * per repo).
+     *
+     * Undefined ≡ `application` for policy resolution, but is preserved
+     * as `undefined` in `ScanMeta` so consumers can distinguish "no flag
+     * passed" from "explicit --cluster-policy application".
+     */
+    contextProfile?: ContextProfile;
 }
 export interface ScanProgress {
     phase: 'clone' | 'discover' | 'analyze' | 'report';
@@ -100,6 +132,24 @@ export interface ScanResult {
      * error). Always present, may be empty. JSON-stable.
      */
     parseFailures: ParseFailure[];
+    /**
+     * cognium-ai#154 (L5c) — top-level cluster assignments computed once
+     * per scan by `runClusterPass()`. The k-medoids result is a pure
+     * function of each file's CK + import/annotation fingerprint;
+     * downstream consumers (health, action-queue, cognium-ai formatters)
+     * can read `medoids[]` for representative files without re-running
+     * the pass.
+     *
+     * Absent when:
+     *   - no successful file results (all parse-failed or pre-flight-skipped);
+     *   - `LLM_CLUSTER_CACHE=0` AND fewer than 2 files (k-medoids requires
+     *     at least 2 inputs to be meaningful).
+     *
+     * Per-file `clusterId` is threaded onto `FileResult.clusterId` so
+     * callers that only care about a single file's cluster don't need to
+     * index into this array.
+     */
+    clusters?: ClusterResult;
 }
 export interface ScanMeta {
     /** Target repository or path */
@@ -114,6 +164,14 @@ export interface ScanMeta {
     durationMs: number;
     /** Circle-IR version */
     version: string;
+    /**
+     * cognium-ai#154 (L5c) — resolved context profile for the scan.
+     * Mirrors the caller's `ScanOptions.contextProfile` verbatim (undefined
+     * when the caller didn't pass `--cluster-policy`, distinguishing "no
+     * flag" from "explicit --cluster-policy application"). Consumed by
+     * top-100 sweep telemetry per operating principle P2.
+     */
+    contextProfile?: ContextProfile;
 }
 export interface ScanFinding extends Finding {
     /** OWASP Top 10 mapping */
@@ -188,6 +246,24 @@ export interface FileResult {
     skipped?: {
         reason: string;
     };
+    /**
+     * cognium-ai#154 (L5c) — k-medoids cluster id assigned by
+     * `runClusterPass()`. Absent on parseFailure / preFlightSkip rows
+     * (they never produced a ClusterVector), and absent when
+     * `ScanResult.clusters` itself is absent (see that field for the
+     * fallback conditions).
+     */
+    clusterId?: number;
+    /**
+     * cognium-ai#154 (L5c) — internal transport for the CK +
+     * import/annotation fingerprint from `analyzeFile()` / `analyzeFileWithLLM()`
+     * up to `runClusterPass()`. Stripped in `generateReport()` before
+     * emit; downstream JSON consumers should never see it. Kept optional
+     * so parse-failure rows deserialize cleanly.
+     *
+     * @internal
+     */
+    clusterVector?: ClusterVector;
 }
 export declare class SecurityScanner {
     private workDir;
@@ -222,6 +298,19 @@ export declare class SecurityScanner {
      * `undefined` is permitted — the cache falls through to `_unowned`.
      */
     private scanCoordinate?;
+    /**
+     * cognium-ai#154 (L5c) — per-cluster policy overrides. Populated in
+     * `scan()` from `ScanOptions.clusterPolicies`; consumed by
+     * `applyClusterPolicies()` after `runClusterPass()`.
+     */
+    private clusterPolicies?;
+    /**
+     * cognium-ai#154 (L5c) — resolved uniform context profile. Populated
+     * in `scan()` from `ScanOptions.contextProfile`; consumed by
+     * `applyClusterPolicies()` as the fallback when no per-cluster policy
+     * is set. Also echoed into `ScanMeta.contextProfile`.
+     */
+    private contextProfile?;
     constructor();
     /**
      * Run a security scan on a repository or local path.
@@ -269,6 +358,58 @@ export declare class SecurityScanner {
      * Check if severity meets minimum threshold.
      */
     private meetsMinSeverity;
+    /**
+     * cognium-ai#154 (L5c) — top-level k-medoids cluster pass.
+     *
+     * Runs once per scan, after all per-file `analyze()` calls have
+     * populated `fileResults[*].clusterVector`. Never throws — a failure
+     * anywhere in this method leaves `clusterId` unset on every row and
+     * returns `undefined` so `ScanResult.clusters` is absent. That's the
+     * "no cluster policy applied" state, which is byte-identical to
+     * pre-2.33.0 behaviour.
+     *
+     * Cache: keys on the CK-vector signature + rule-set fingerprint + k;
+     * warm re-scans on the same repo (7-day TTL) skip the O(n²) distance
+     * matrix + swap phase entirely. Miss cost is dominated by the k-medoids
+     * pass itself which is <2s at 5000 files per `cluster.ts:355-359`.
+     *
+     * k-selection: `min(8, ceil(sqrt(n)))` — sqrt-heuristic is standard
+     * for k-medoids without ground truth; cap 8 keeps per-cluster policy
+     * manageable and avoids over-partitioning small repos. n<2 returns
+     * `undefined` (k-medoids requires at least 2 inputs).
+     */
+    private runClusterPass;
+    /**
+     * cognium-ai#154 (L5c) — post-hoc cluster-policy filter.
+     *
+     * Iterates every `FileResult` with a resolved `clusterId` and applies
+     * the policy attached to that cluster:
+     *
+     *   1. Per-cluster override in `this.clusterPolicies` wins;
+     *   2. Uniform profile in `this.contextProfile` fires when no
+     *      per-cluster override exists;
+     *   3. Otherwise `DEFAULT_CLUSTER_POLICY` (no-op filter).
+     *
+     * **What the filter does today (L5c):** applies
+     * `policy.sinkWhitelist` post-hoc. When the whitelist is non-empty,
+     * only findings whose vulnerability `type` matches one of the
+     * whitelisted sink classes survive. Empty whitelist ≡ pass-through.
+     *
+     * **What is deferred to L5d (documented no-ops today):**
+     *   - `policy.sourceWhitelist` — requires a discovery-source tag on
+     *     `Finding` we don't currently carry through the workflow. Wiring
+     *     the tag needs a signature change in `runEnrich` / `runVerify`
+     *     that L5c deliberately avoids.
+     *   - `policy.llmEnabled === false` — post-hoc, LLM findings have
+     *     already been produced (and paid for). Dropping them here saves
+     *     no LLM calls; the intent-signal version belongs in a pre-LLM
+     *     pass in `analyzeFiles()` (L5d).
+     *
+     * Never throws — the same never-throw contract as `runClusterPass()`.
+     * Files with `clusterId === undefined` (parse failures, pre-flight
+     * skips, or `ScanResult.clusters` absent) are untouched.
+     */
+    private applyClusterPolicies;
     /**
      * Generate scan report.
      */

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