gitnexus 1.6.3-rc.14 → 1.6.3-rc.16

package/dist/_shared/graph/types.d.ts

@@ -61,5 +61,21 @@ export interface GraphRelationship {
     confidence: number;
     reason: string;
     step?: number;
+    /**
+     * Per-signal evidence trace for edges emitted by the scope-based
+     * resolution pipeline (RFC #909 Ring 2 PKG #925). Populated by
+     * `emit-references.ts` when draining `ReferenceIndex` into the graph
+     * so downstream query / audit tools can inspect *why* a given edge
+     * was emitted with its confidence value.
+     *
+     * Optional and additive — every existing edge emitter ignores this
+     * field, and every existing query continues to work whether or not
+     * an edge carries it.
+     */
+    evidence?: readonly {
+        readonly kind: string;
+        readonly weight: number;
+        readonly note?: string;
+    }[];
 }
 //# sourceMappingURL=types.d.ts.map

package/dist/_shared/graph/types.d.ts.map

@@ -1 +1 @@
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package/dist/core/ingestion/emit-references.d.ts

@@ -0,0 +1,88 @@
+/**
+ * Phase 5 of the RFC #909 ingestion lifecycle: drain `ReferenceIndex`
+ * into the knowledge graph as labeled edges with `confidence` and
+ * `evidence` properties (Ring 2 PKG #925).
+ *
+ * The resolution phase (future PR) writes `Reference` records into
+ * `model.scopes.referenceSites`-derived `ReferenceIndex`; this module
+ * materializes those records as `GraphRelationship`s via
+ * `graph.addRelationship`. Every emitted edge carries:
+ *
+ *   - `type`: one of `'CALLS' | 'ACCESSES' | 'INHERITS' | 'USES'`
+ *     (mapped from `Reference.kind` — `'read'` and `'write'` both route
+ *     to `ACCESSES`; `'type-reference'` and `'import-use'` route to
+ *     `USES`; `'call'` stays `CALLS`; `'inherits'` stays `INHERITS`).
+ *   - `confidence`: the pre-computed confidence from the Reference record.
+ *   - `reason`: human-readable summary (`"scope-resolution: call | confidence 0.75"`).
+ *   - `evidence`: the full `ResolutionEvidence[]` trace — additive graph
+ *     property (see `GraphRelationship.evidence` in gitnexus-shared),
+ *     so queries that don't know about it are unaffected.
+ *   - `step`: carries the reference's access-kind discriminant when
+ *     available (`1` for read, `2` for write) so `ACCESSES` edges retain
+ *     the read/write distinction without forcing a new edge type.
+ *
+ * ## Optional scope-tree flush
+ *
+ * When `INGESTION_EMIT_SCOPES=1` is set, this module also emits:
+ *
+ *   - `Scope` nodes for every `Scope` in the tree
+ *   - `CONTAINS` edges from parent scope to child scope
+ *   - `DEFINES` edges from scope to its `ownedDefs` members
+ *   - `IMPORTS` edges from scope to `targetModuleScope` of each finalized
+ *     `ImportEdge` that carries one
+ *
+ * Off by default — existing queries that don't know about `Scope` nodes
+ * continue to work, and the storage cost is opt-in.
+ *
+ * ## Source-of-truth: the caller def for a reference
+ *
+ * A `Reference` says "some code inside `fromScope` references `toDef`".
+ * The graph wants `(callerNodeId, calleeNodeId)`. We resolve the caller
+ * by walking up the scope tree from `fromScope` until we find a scope
+ * whose `ownedDefs` contains a Function-like def. If no such ancestor
+ * exists, the edge is attributed to the first def owned by the innermost
+ * ancestor scope, and if THAT produces nothing either the edge is
+ * skipped (with a count returned in `EmitStats.skippedNoCaller`).
+ */
+import type { ReferenceIndex } from '../../_shared/index.js';
+import type { KnowledgeGraph } from '../graph/types.js';
+import type { ScopeResolutionIndexes } from './model/scope-resolution-indexes.js';
+export interface EmitStats {
+    readonly edgesEmitted: number;
+    /** References dropped because no caller def could be resolved. */
+    readonly skippedNoCaller: number;
+    /** References dropped because `toDef` was not found in the DefIndex. */
+    readonly skippedMissingTarget: number;
+    /** Scope nodes emitted — `0` unless `INGESTION_EMIT_SCOPES=1`. */
+    readonly scopeNodesEmitted: number;
+    /** Scope-tree structural edges emitted — `0` unless `INGESTION_EMIT_SCOPES=1`. */
+    readonly scopeEdgesEmitted: number;
+}
+export interface EmitReferencesInput {
+    readonly graph: KnowledgeGraph;
+    readonly scopes: ScopeResolutionIndexes;
+    readonly referenceIndex: ReferenceIndex;
+    /** Human-consumable label for the `reason` prefix. Defaults to `'scope-resolution'`. */
+    readonly sourceLabel?: string;
+}
+/**
+ * Drain `referenceIndex.bySourceScope` into graph edges.
+ *
+ * The scope-tree flush is controlled separately by
+ * `INGESTION_EMIT_SCOPES` — callers can run `emitReferencesToGraph`
+ * without scope-node emission or layer the two calls as needed.
+ */
+export declare function emitReferencesToGraph(input: EmitReferencesInput): EmitStats;
+/**
+ * Emit `Scope` nodes + `CONTAINS`/`DEFINES`/`IMPORTS` edges representing
+ * the lexical scope tree itself. Skipped unless `INGESTION_EMIT_SCOPES=1`
+ * at the public entry point; exported here for tests that want to
+ * exercise the path directly.
+ */
+export declare function emitScopeGraph(input: {
+    readonly graph: KnowledgeGraph;
+    readonly scopes: ScopeResolutionIndexes;
+}): {
+    readonly scopeNodesEmitted: number;
+    readonly scopeEdgesEmitted: number;
+};

package/dist/core/ingestion/emit-references.js

@@ -0,0 +1,229 @@
+/**
+ * Phase 5 of the RFC #909 ingestion lifecycle: drain `ReferenceIndex`
+ * into the knowledge graph as labeled edges with `confidence` and
+ * `evidence` properties (Ring 2 PKG #925).
+ *
+ * The resolution phase (future PR) writes `Reference` records into
+ * `model.scopes.referenceSites`-derived `ReferenceIndex`; this module
+ * materializes those records as `GraphRelationship`s via
+ * `graph.addRelationship`. Every emitted edge carries:
+ *
+ *   - `type`: one of `'CALLS' | 'ACCESSES' | 'INHERITS' | 'USES'`
+ *     (mapped from `Reference.kind` — `'read'` and `'write'` both route
+ *     to `ACCESSES`; `'type-reference'` and `'import-use'` route to
+ *     `USES`; `'call'` stays `CALLS`; `'inherits'` stays `INHERITS`).
+ *   - `confidence`: the pre-computed confidence from the Reference record.
+ *   - `reason`: human-readable summary (`"scope-resolution: call | confidence 0.75"`).
+ *   - `evidence`: the full `ResolutionEvidence[]` trace — additive graph
+ *     property (see `GraphRelationship.evidence` in gitnexus-shared),
+ *     so queries that don't know about it are unaffected.
+ *   - `step`: carries the reference's access-kind discriminant when
+ *     available (`1` for read, `2` for write) so `ACCESSES` edges retain
+ *     the read/write distinction without forcing a new edge type.
+ *
+ * ## Optional scope-tree flush
+ *
+ * When `INGESTION_EMIT_SCOPES=1` is set, this module also emits:
+ *
+ *   - `Scope` nodes for every `Scope` in the tree
+ *   - `CONTAINS` edges from parent scope to child scope
+ *   - `DEFINES` edges from scope to its `ownedDefs` members
+ *   - `IMPORTS` edges from scope to `targetModuleScope` of each finalized
+ *     `ImportEdge` that carries one
+ *
+ * Off by default — existing queries that don't know about `Scope` nodes
+ * continue to work, and the storage cost is opt-in.
+ *
+ * ## Source-of-truth: the caller def for a reference
+ *
+ * A `Reference` says "some code inside `fromScope` references `toDef`".
+ * The graph wants `(callerNodeId, calleeNodeId)`. We resolve the caller
+ * by walking up the scope tree from `fromScope` until we find a scope
+ * whose `ownedDefs` contains a Function-like def. If no such ancestor
+ * exists, the edge is attributed to the first def owned by the innermost
+ * ancestor scope, and if THAT produces nothing either the edge is
+ * skipped (with a count returned in `EmitStats.skippedNoCaller`).
+ */
+/**
+ * Drain `referenceIndex.bySourceScope` into graph edges.
+ *
+ * The scope-tree flush is controlled separately by
+ * `INGESTION_EMIT_SCOPES` — callers can run `emitReferencesToGraph`
+ * without scope-node emission or layer the two calls as needed.
+ */
+export function emitReferencesToGraph(input) {
+    const { graph, scopes, referenceIndex } = input;
+    const sourceLabel = input.sourceLabel ?? 'scope-resolution';
+    let edgesEmitted = 0;
+    let skippedNoCaller = 0;
+    let skippedMissingTarget = 0;
+    for (const [fromScope, refs] of referenceIndex.bySourceScope) {
+        for (const ref of refs) {
+            const targetDef = scopes.defs.get(ref.toDef);
+            if (targetDef === undefined) {
+                skippedMissingTarget++;
+                continue;
+            }
+            const callerId = resolveCallerNodeId(fromScope, scopes);
+            if (callerId === undefined) {
+                skippedNoCaller++;
+                continue;
+            }
+            graph.addRelationship(buildRelationship(ref, callerId, targetDef, sourceLabel));
+            edgesEmitted++;
+        }
+    }
+    const scopeStats = isScopeEmissionEnabled()
+        ? emitScopeGraph({ graph, scopes })
+        : { scopeNodesEmitted: 0, scopeEdgesEmitted: 0 };
+    return { edgesEmitted, skippedNoCaller, skippedMissingTarget, ...scopeStats };
+}
+/**
+ * Emit `Scope` nodes + `CONTAINS`/`DEFINES`/`IMPORTS` edges representing
+ * the lexical scope tree itself. Skipped unless `INGESTION_EMIT_SCOPES=1`
+ * at the public entry point; exported here for tests that want to
+ * exercise the path directly.
+ */
+export function emitScopeGraph(input) {
+    const { graph, scopes } = input;
+    let scopeNodesEmitted = 0;
+    let scopeEdgesEmitted = 0;
+    for (const scope of scopes.scopeTree.byId.values()) {
+        graph.addNode({
+            id: scope.id,
+            label: 'CodeElement', // the generic bucket for non-symbol graph nodes
+            properties: {
+                name: scope.kind,
+                filePath: scope.filePath,
+                startLine: scope.range.startLine,
+                endLine: scope.range.endLine,
+                description: `Scope: ${scope.kind}`,
+            },
+        });
+        scopeNodesEmitted++;
+        if (scope.parent !== null) {
+            graph.addRelationship({
+                id: `rel:contains:${scope.parent}->${scope.id}`,
+                sourceId: scope.parent,
+                targetId: scope.id,
+                type: 'CONTAINS',
+                confidence: 1,
+                reason: 'scope-tree parent/child',
+            });
+            scopeEdgesEmitted++;
+        }
+        for (const def of scope.ownedDefs) {
+            graph.addRelationship({
+                id: `rel:defines:${scope.id}->${def.nodeId}`,
+                sourceId: scope.id,
+                targetId: def.nodeId,
+                type: 'DEFINES',
+                confidence: 1,
+                reason: 'scope.ownedDefs',
+            });
+            scopeEdgesEmitted++;
+        }
+    }
+    for (const [scopeId, edges] of scopes.imports) {
+        for (const edge of edges) {
+            if (edge.targetModuleScope === undefined)
+                continue;
+            graph.addRelationship({
+                id: `rel:imports:${scopeId}->${edge.targetModuleScope}:${edge.localName}`,
+                sourceId: scopeId,
+                targetId: edge.targetModuleScope,
+                type: 'IMPORTS',
+                confidence: edge.linkStatus === 'unresolved' ? 0.5 : 1,
+                reason: `import ${edge.kind} ${edge.localName}`,
+            });
+            scopeEdgesEmitted++;
+        }
+    }
+    return { scopeNodesEmitted, scopeEdgesEmitted };
+}
+// ─── Internal ───────────────────────────────────────────────────────────────
+/** Accepted truthy values for `INGESTION_EMIT_SCOPES`. */
+const TRUTHY = new Set(['true', '1', 'yes']);
+function isScopeEmissionEnabled() {
+    const raw = process.env['INGESTION_EMIT_SCOPES'];
+    if (raw === undefined)
+        return false;
+    return TRUTHY.has(raw.trim().toLowerCase());
+}
+/**
+ * Walk up from `startScope` looking for the first ancestor scope whose
+ * `ownedDefs` contains a Function-like def (Function / Method /
+ * Constructor). Fall back to the innermost ancestor's first `ownedDef`
+ * if none is found; return `undefined` if all ancestors have no defs.
+ */
+function resolveCallerNodeId(startScope, scopes) {
+    const tree = scopes.scopeTree;
+    let current = startScope;
+    const visited = new Set();
+    let firstOwnedFallback;
+    while (current !== null) {
+        if (visited.has(current))
+            break;
+        visited.add(current);
+        const scope = tree.getScope(current);
+        if (scope === undefined)
+            break;
+        // Prefer a Function-like owner.
+        const fnDef = scope.ownedDefs.find((d) => isFunctionLike(d.type));
+        if (fnDef !== undefined)
+            return fnDef.nodeId;
+        // Stash the first owned def we see as a conservative fallback.
+        if (firstOwnedFallback === undefined && scope.ownedDefs.length > 0) {
+            firstOwnedFallback = scope.ownedDefs[0].nodeId;
+        }
+        current = scope.parent;
+    }
+    return firstOwnedFallback;
+}
+function isFunctionLike(type) {
+    return type === 'Function' || type === 'Method' || type === 'Constructor';
+}
+function buildRelationship(ref, callerId, targetDef, sourceLabel) {
+    const type = mapKindToType(ref.kind);
+    const reason = `${sourceLabel}: ${ref.kind} | confidence ${ref.confidence.toFixed(3)}`;
+    // `step` encodes read/write discriminator for ACCESSES edges (1=read, 2=write).
+    // Other kinds omit `step`.
+    const step = ref.kind === 'read' ? 1 : ref.kind === 'write' ? 2 : undefined;
+    return {
+        id: `rel:${type}:${callerId}->${targetDef.nodeId}:${ref.atRange.startLine}:${ref.atRange.startCol}`,
+        sourceId: callerId,
+        targetId: targetDef.nodeId,
+        type,
+        confidence: ref.confidence,
+        reason,
+        evidence: ref.evidence.map(serializeEvidence),
+        ...(step !== undefined ? { step } : {}),
+    };
+}
+/**
+ * Map a `Reference.kind` to an existing `RelationshipType`. Read/write
+ * both fold into `ACCESSES`; `type-reference` + `import-use` both fold
+ * into `USES`. This keeps the graph schema additive — no new
+ * RelationshipType values are introduced by this module.
+ */
+function mapKindToType(kind) {
+    switch (kind) {
+        case 'call':
+            return 'CALLS';
+        case 'read':
+        case 'write':
+            return 'ACCESSES';
+        case 'inherits':
+            return 'INHERITS';
+        case 'type-reference':
+        case 'import-use':
+            return 'USES';
+    }
+}
+function serializeEvidence(e) {
+    return {
+        kind: e.kind,
+        weight: e.weight,
+        ...(e.note !== undefined ? { note: e.note } : {}),
+    };
+}

package/dist/core/ingestion/shadow-harness.d.ts

@@ -0,0 +1,113 @@
+/**
+ * Shadow-mode parity harness — dual-run observability for the RFC #909
+ * registry rollout (RFC §6.3; Ring 2 PKG #923).
+ *
+ * ## What it does
+ *
+ *   - Exposes `record({ language, callsite, legacy, newResult })` for
+ *     every call site where the caller has BOTH a legacy-DAG resolution
+ *     and a new `Registry.lookup` resolution.
+ *   - Computes a `ShadowDiff` per record via shared `diffResolutions`
+ *     (#918) and accumulates them in a per-language bucket.
+ *   - At the end of a run, aggregates into a `ShadowParityReport` via
+ *     shared `aggregateDiffs` (#918) — per-language parity %,
+ *     evidence-kind breakdown of divergences, grand-total overall row.
+ *   - Optionally persists the report as JSON under
+ *     `.gitnexus/shadow-parity/` so the static dashboard at
+ *     `gitnexus/shadow-parity-dashboard/` can render it offline.
+ *
+ * ## What it does NOT do
+ *
+ *   - **Invoke either resolution path itself.** The caller must run
+ *     legacy + `Registry.lookup` and pass results in. The harness is a
+ *     side-car, not a dispatcher — this keeps call-processor integration
+ *     surgical when it lands (tracked as a follow-up; the shared model
+ *     doesn't dual-invoke on its own).
+ *   - **Flip anything.** `REGISTRY_PRIMARY_<LANG>` lives in
+ *     `registry-primary-flag.ts` (#924); the harness records the
+ *     caller-supplied "which side is primary" bit for each record so the
+ *     dashboard can label rows, but it does not consult the flag itself.
+ *
+ * ## Activation
+ *
+ * `GITNEXUS_SHADOW_MODE=1` (or `'true'`, `'yes'`, case-insensitive,
+ * trimmed) enables the harness. When disabled, `record()` is a cheap
+ * no-op: no accumulation, no allocation beyond the harness object
+ * itself. Callers can always construct a harness and hand it through;
+ * the "off" overhead is near-zero.
+ *
+ * ## Persistence shape
+ *
+ * When `persist()` is called, the harness writes TWO files:
+ *
+ *   - `<outputDir>/<runId>.json` — the timestamped snapshot (immutable)
+ *   - `<outputDir>/latest.json`  — a pointer that the dashboard reads
+ *
+ * Both files contain the same `PersistedShadowReport` payload:
+ *
+ *   {
+ *     schemaVersion: 1,
+ *     runId: "<iso-8601>-<rand>",
+ *     generatedAt: "<iso-8601>",
+ *     primaryByLanguage: { [lang]: "legacy" | "registry" },
+ *     report: <ShadowParityReport>
+ *   }
+ *
+ * Schema-version-gated so future format changes don't silently confuse
+ * older dashboards. The dashboard renders `report.perLanguage` rows and
+ * annotates each with `primaryByLanguage[lang]`.
+ */
+import { type Resolution, type ShadowCallsite, type ShadowParityReport, type SupportedLanguages } from '../../_shared/index.js';
+/** Which side of the dual-run is considered authoritative for this language. */
+export type PrimarySide = 'legacy' | 'registry';
+/** One record per call site the caller dual-runs. */
+export interface ShadowRecordInput {
+    readonly language: SupportedLanguages;
+    readonly callsite: ShadowCallsite;
+    readonly legacy: readonly Resolution[];
+    readonly newResult: readonly Resolution[];
+    /**
+     * Which side drove the actual runtime answer for this record. Lets the
+     * dashboard distinguish "registry-primary, legacy is shadow" from the
+     * default "legacy-primary, registry is shadow" without re-reading
+     * `REGISTRY_PRIMARY_<LANG>` env vars at render time.
+     */
+    readonly primary: PrimarySide;
+}
+/** Persisted JSON shape. Schema-versioned for future migrations. */
+export interface PersistedShadowReport {
+    readonly schemaVersion: 1;
+    readonly runId: string;
+    readonly generatedAt: string;
+    readonly primaryByLanguage: Readonly<Partial<Record<SupportedLanguages, PrimarySide>>>;
+    readonly report: ShadowParityReport;
+}
+export interface ShadowHarness {
+    /** `true` iff `GITNEXUS_SHADOW_MODE` is truthy. When `false`, `record()` is a no-op. */
+    readonly enabled: boolean;
+    /** Accumulate a dual-run observation. No-op when `enabled === false`. */
+    record(input: ShadowRecordInput): void;
+    /** Number of records accumulated so far. Useful for diagnostics / tests. */
+    size(): number;
+    /**
+     * Aggregate the accumulated records into a `ShadowParityReport`
+     * without persisting. Returns a deterministic snapshot each call;
+     * idempotent with respect to `record()` ordering.
+     */
+    snapshot(now?: Date): ShadowParityReport;
+    /**
+     * Write the aggregated snapshot to JSON. Resolves to the path of the
+     * per-run file. Also writes/overwrites `latest.json` alongside.
+     *
+     * Creates `outputDir` if it doesn't exist.
+     */
+    persist(outputDir: string, now?: Date): Promise<string>;
+    /** Reset the accumulator. Preserves `enabled`. */
+    clear(): void;
+}
+/**
+ * Construct a harness. Reads `GITNEXUS_SHADOW_MODE` at construction time
+ * (not per-`record()` call) so repeated no-op records don't re-check the
+ * env var in the hot path.
+ */
+export declare function createShadowHarness(): ShadowHarness;

package/dist/core/ingestion/shadow-harness.js

@@ -0,0 +1,148 @@
+/**
+ * Shadow-mode parity harness — dual-run observability for the RFC #909
+ * registry rollout (RFC §6.3; Ring 2 PKG #923).
+ *
+ * ## What it does
+ *
+ *   - Exposes `record({ language, callsite, legacy, newResult })` for
+ *     every call site where the caller has BOTH a legacy-DAG resolution
+ *     and a new `Registry.lookup` resolution.
+ *   - Computes a `ShadowDiff` per record via shared `diffResolutions`
+ *     (#918) and accumulates them in a per-language bucket.
+ *   - At the end of a run, aggregates into a `ShadowParityReport` via
+ *     shared `aggregateDiffs` (#918) — per-language parity %,
+ *     evidence-kind breakdown of divergences, grand-total overall row.
+ *   - Optionally persists the report as JSON under
+ *     `.gitnexus/shadow-parity/` so the static dashboard at
+ *     `gitnexus/shadow-parity-dashboard/` can render it offline.
+ *
+ * ## What it does NOT do
+ *
+ *   - **Invoke either resolution path itself.** The caller must run
+ *     legacy + `Registry.lookup` and pass results in. The harness is a
+ *     side-car, not a dispatcher — this keeps call-processor integration
+ *     surgical when it lands (tracked as a follow-up; the shared model
+ *     doesn't dual-invoke on its own).
+ *   - **Flip anything.** `REGISTRY_PRIMARY_<LANG>` lives in
+ *     `registry-primary-flag.ts` (#924); the harness records the
+ *     caller-supplied "which side is primary" bit for each record so the
+ *     dashboard can label rows, but it does not consult the flag itself.
+ *
+ * ## Activation
+ *
+ * `GITNEXUS_SHADOW_MODE=1` (or `'true'`, `'yes'`, case-insensitive,
+ * trimmed) enables the harness. When disabled, `record()` is a cheap
+ * no-op: no accumulation, no allocation beyond the harness object
+ * itself. Callers can always construct a harness and hand it through;
+ * the "off" overhead is near-zero.
+ *
+ * ## Persistence shape
+ *
+ * When `persist()` is called, the harness writes TWO files:
+ *
+ *   - `<outputDir>/<runId>.json` — the timestamped snapshot (immutable)
+ *   - `<outputDir>/latest.json`  — a pointer that the dashboard reads
+ *
+ * Both files contain the same `PersistedShadowReport` payload:
+ *
+ *   {
+ *     schemaVersion: 1,
+ *     runId: "<iso-8601>-<rand>",
+ *     generatedAt: "<iso-8601>",
+ *     primaryByLanguage: { [lang]: "legacy" | "registry" },
+ *     report: <ShadowParityReport>
+ *   }
+ *
+ * Schema-version-gated so future format changes don't silently confuse
+ * older dashboards. The dashboard renders `report.perLanguage` rows and
+ * annotates each with `primaryByLanguage[lang]`.
+ */
+import * as fs from 'node:fs/promises';
+import * as path from 'node:path';
+import { aggregateDiffs, diffResolutions, } from '../../_shared/index.js';
+/**
+ * Construct a harness. Reads `GITNEXUS_SHADOW_MODE` at construction time
+ * (not per-`record()` call) so repeated no-op records don't re-check the
+ * env var in the hot path.
+ */
+export function createShadowHarness() {
+    const enabled = parseShadowModeEnv(process.env['GITNEXUS_SHADOW_MODE']);
+    const records = [];
+    const primaryByLanguage = {};
+    const recordImpl = (input) => {
+        if (!enabled)
+            return;
+        const diff = diffResolutions(input.callsite, input.legacy, input.newResult);
+        records.push({ language: input.language, diff });
+        // Primary per-language is resolved by last-write. In practice a run
+        // is single-threaded with respect to flag readings, so this is
+        // deterministic; a language's primary cannot change mid-run.
+        primaryByLanguage[input.language] = input.primary;
+    };
+    const snapshotImpl = (now = new Date()) => {
+        return aggregateDiffs(records, now);
+    };
+    const persistImpl = async (outputDir, now = new Date()) => {
+        await fs.mkdir(outputDir, { recursive: true });
+        const report = snapshotImpl(now);
+        const runId = makeRunId(now);
+        const payload = {
+            schemaVersion: 1,
+            runId,
+            generatedAt: now.toISOString(),
+            primaryByLanguage,
+            report,
+        };
+        const json = JSON.stringify(payload, null, 2);
+        const perRunPath = path.join(outputDir, `${runId}.json`);
+        const latestPath = path.join(outputDir, 'latest.json');
+        await fs.writeFile(perRunPath, json, 'utf8');
+        await fs.writeFile(latestPath, json, 'utf8');
+        return perRunPath;
+    };
+    const clearImpl = () => {
+        records.length = 0;
+        for (const key of Object.keys(primaryByLanguage)) {
+            delete primaryByLanguage[key];
+        }
+    };
+    return {
+        enabled,
+        record: recordImpl,
+        size: () => records.length,
+        snapshot: snapshotImpl,
+        persist: persistImpl,
+        clear: clearImpl,
+    };
+}
+// ─── Internal helpers ─────────────────────────────────────────────────────
+/**
+ * Env-var parser for `GITNEXUS_SHADOW_MODE`. Accepts the same truthy
+ * conventions as `REGISTRY_PRIMARY_<LANG>` from #924: `'true'` / `'1'` /
+ * `'yes'`, case-insensitive, whitespace-trimmed. Anything else — including
+ * `undefined`, `''`, `'false'`, `'off'`, typos — is false.
+ */
+function parseShadowModeEnv(raw) {
+    if (raw === undefined)
+        return false;
+    const normalized = raw.trim().toLowerCase();
+    return normalized === 'true' || normalized === '1' || normalized === 'yes';
+}
+/**
+ * Deterministic run id derived from the timestamp plus 4 random bytes
+ * of entropy. The timestamp comes first so files sort chronologically;
+ * the entropy suffix prevents collisions when multiple runs share a
+ * clock-second. Shape: `YYYYMMDD-HHMMSS-xxxxxxxx`.
+ */
+function makeRunId(now) {
+    const y = now.getUTCFullYear().toString().padStart(4, '0');
+    const m = (now.getUTCMonth() + 1).toString().padStart(2, '0');
+    const d = now.getUTCDate().toString().padStart(2, '0');
+    const h = now.getUTCHours().toString().padStart(2, '0');
+    const min = now.getUTCMinutes().toString().padStart(2, '0');
+    const s = now.getUTCSeconds().toString().padStart(2, '0');
+    const entropy = Math.floor(Math.random() * 0xffffffff)
+        .toString(16)
+        .padStart(8, '0');
+    return `${y}${m}${d}-${h}${min}${s}-${entropy}`;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.3-rc.14",
+  "version": "1.6.3-rc.16",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",