@cleocode/core 2026.4.30 → 2026.4.35

package/dist/store/nexus-schema.js

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+/**
+ * Drizzle ORM schema for CLEO nexus.db (SQLite via node:sqlite + sqlite-proxy).
+ *
+ * Tables: project_registry, nexus_audit_log, nexus_schema_meta,
+ *         nexus_nodes, nexus_relations
+ * Stores cross-project registry and audit infrastructure for the Nexus domain,
+ * plus the code intelligence graph layer (nodes + directed edges).
+ *
+ * @task T5365
+ * @task T529
+ */
+import { sql } from 'drizzle-orm';
+import { index, integer, real, sqliteTable, text } from 'drizzle-orm/sqlite-core';
+// === PROJECT_REGISTRY TABLE ===
+/** Central registry of all CLEO projects known to the Nexus. */
+export const projectRegistry = sqliteTable('project_registry', {
+    projectId: text('project_id').primaryKey(),
+    projectHash: text('project_hash').notNull().unique(),
+    projectPath: text('project_path').notNull().unique(),
+    name: text('name').notNull(),
+    registeredAt: text('registered_at').notNull().default(sql `(datetime('now'))`),
+    lastSeen: text('last_seen').notNull().default(sql `(datetime('now'))`),
+    healthStatus: text('health_status').notNull().default('unknown'),
+    healthLastCheck: text('health_last_check'),
+    permissions: text('permissions').notNull().default('read'),
+    lastSync: text('last_sync').notNull().default(sql `(datetime('now'))`),
+    taskCount: integer('task_count').notNull().default(0),
+    labelsJson: text('labels_json').notNull().default('[]'),
+}, (table) => [
+    index('idx_project_registry_hash').on(table.projectHash),
+    index('idx_project_registry_health').on(table.healthStatus),
+    index('idx_project_registry_name').on(table.name),
+]);
+// === NEXUS_AUDIT_LOG TABLE ===
+/** Append-only audit log for all Nexus operations across projects. */
+export const nexusAuditLog = sqliteTable('nexus_audit_log', {
+    id: text('id').primaryKey(),
+    timestamp: text('timestamp').notNull().default(sql `(datetime('now'))`),
+    action: text('action').notNull(),
+    projectHash: text('project_hash'),
+    projectId: text('project_id'),
+    domain: text('domain'),
+    operation: text('operation'),
+    sessionId: text('session_id'),
+    requestId: text('request_id'),
+    source: text('source'),
+    gateway: text('gateway'),
+    success: integer('success'),
+    durationMs: integer('duration_ms'),
+    detailsJson: text('details_json').default('{}'),
+    errorMessage: text('error_message'),
+}, (table) => [
+    index('idx_nexus_audit_timestamp').on(table.timestamp),
+    index('idx_nexus_audit_action').on(table.action),
+    index('idx_nexus_audit_project_hash').on(table.projectHash),
+    index('idx_nexus_audit_project_id').on(table.projectId),
+    index('idx_nexus_audit_session').on(table.sessionId),
+]);
+// === SCHEMA METADATA ===
+/** Key-value store for nexus.db schema versioning and metadata. */
+export const nexusSchemaMeta = sqliteTable('nexus_schema_meta', {
+    key: text('key').primaryKey(),
+    value: text('value').notNull(),
+});
+// === NEXUS_NODES TABLE ===
+/**
+ * All node kind values — matches GraphNodeKind in @cleocode/contracts.
+ *
+ * Kept as a const tuple for use in Drizzle enum column definitions.
+ * The ordering is intentional: structural → module → callable → type →
+ * value-level → language-specific → graph-level → legacy.
+ */
+export const NEXUS_NODE_KINDS = [
+    // Structural
+    'file',
+    'folder',
+    // Module-level
+    'module',
+    'namespace',
+    // Callable
+    'function',
+    'method',
+    'constructor',
+    // Type hierarchy
+    'class',
+    'interface',
+    'struct',
+    'trait',
+    'impl',
+    'type_alias',
+    'enum',
+    // Value-level
+    'property',
+    'constant',
+    'variable',
+    'static',
+    'record',
+    'delegate',
+    // Language-specific constructs
+    'macro',
+    'union',
+    'typedef',
+    'annotation',
+    'template',
+    // Graph-level (synthetic nodes from analysis phases)
+    'community',
+    'process',
+    'route',
+    // External references
+    'tool',
+    'section',
+    // Legacy (kept for T506 compatibility)
+    'import',
+    'export',
+    'type',
+];
+/**
+ * Graph nodes table — one row per symbol or structural element.
+ *
+ * Stores all code intelligence graph nodes indexed per project.
+ * Synthetic nodes (community, process) share this table with
+ * source-derived nodes (function, class, file).
+ *
+ * Both this table and `code_index` are populated from the same parse pass.
+ * They serve complementary roles — do NOT merge them.
+ *
+ * @task T529
+ */
+export const nexusNodes = sqliteTable('nexus_nodes', {
+    /** Stable node ID. Format: `<filePath>::<name>` for symbols,
+     *  `<filePath>` for file nodes, `community:<n>` for community nodes,
+     *  `process:<slug>` for execution flow nodes. */
+    id: text('id').primaryKey(),
+    /** Foreign key to project_registry.project_id. Scopes the node. */
+    projectId: text('project_id').notNull(),
+    /** Node kind from GraphNodeKind union. */
+    kind: text('kind', { enum: NEXUS_NODE_KINDS }).notNull(),
+    /** Human-readable label for display. For symbols, same as name.
+     *  For communities, the inferred folder label. For processes, the
+     *  entry point function name. */
+    label: text('label').notNull(),
+    /** Symbol name as it appears in source code. Null for file/folder nodes. */
+    name: text('name'),
+    /** File path relative to project root. Null for community/process nodes. */
+    filePath: text('file_path'),
+    /** Start line in source file (1-based). Null for structural nodes. */
+    startLine: integer('start_line'),
+    /** End line in source file (1-based). Null for structural nodes. */
+    endLine: integer('end_line'),
+    /** Source language (typescript, python, go, rust, etc.). */
+    language: text('language'),
+    /** Whether the symbol is publicly exported from its module. */
+    isExported: integer('is_exported', { mode: 'boolean' }).notNull().default(false),
+    /** Parent node ID for nested symbols (e.g., method inside class).
+     *  References nexus_nodes.id in the same project. Soft FK. */
+    parentId: text('parent_id'),
+    /** JSON array of parameter name strings for functions/methods.
+     *  Stored as `["param1","param2"]`. Null if not applicable. */
+    parametersJson: text('parameters_json'),
+    /** Return type annotation text (e.g., "Promise<void>"). */
+    returnType: text('return_type'),
+    /** First line of the TSDoc/JSDoc comment for this symbol. */
+    docSummary: text('doc_summary'),
+    /** Community membership ID — references the community node's id.
+     *  Set during Phase 4.5 community detection. Null until then. */
+    communityId: text('community_id'),
+    /** JSON blob for kind-specific metadata.
+     *  For `process` nodes: `{"stepCount": 7, "entryScore": 0.92}`.
+     *  For `community` nodes: `{"memberCount": 14, "topFolders": ["src/core"]}`.
+     *  For `route` nodes: `{"method": "GET", "path": "/api/v1/tasks"}`.
+     *  For all others: null. */
+    metaJson: text('meta_json'),
+    /** ISO 8601 timestamp when this node was last indexed. */
+    indexedAt: text('indexed_at').notNull().default(sql `(datetime('now'))`),
+}, (table) => [
+    index('idx_nexus_nodes_project').on(table.projectId),
+    index('idx_nexus_nodes_kind').on(table.kind),
+    index('idx_nexus_nodes_file').on(table.filePath),
+    index('idx_nexus_nodes_name').on(table.name),
+    index('idx_nexus_nodes_project_kind').on(table.projectId, table.kind),
+    index('idx_nexus_nodes_project_file').on(table.projectId, table.filePath),
+    index('idx_nexus_nodes_community').on(table.communityId),
+    index('idx_nexus_nodes_parent').on(table.parentId),
+    index('idx_nexus_nodes_exported').on(table.isExported),
+]);
+// === NEXUS_RELATIONS TABLE ===
+/**
+ * All relation type values — matches GraphRelationType in @cleocode/contracts.
+ *
+ * Kept as a const tuple for use in Drizzle enum column definitions.
+ */
+export const NEXUS_RELATION_TYPES = [
+    // Structural
+    'contains',
+    // Definition / usage
+    'defines',
+    'imports',
+    'accesses',
+    // Callable
+    'calls',
+    // Type hierarchy
+    'extends',
+    'implements',
+    'method_overrides',
+    'method_implements',
+    // Class structure
+    'has_method',
+    'has_property',
+    // Graph-level (synthetic, from analysis phases)
+    'member_of', // symbol → community
+    'step_in_process', // symbol → process
+    // Web / API
+    'handles_route', // function → route node
+    'fetches', // function → external API
+    // Tool / agent
+    'handles_tool',
+    'entry_point_of', // function → process
+    // Wrapping / delegation
+    'wraps',
+    // Data access
+    'queries',
+    // Cross-graph (brain link)
+    'documents', // brain_page_node → nexus_nodes
+    'applies_to', // brain_page_node → nexus_nodes
+];
+/**
+ * Graph relations table — one row per directed edge.
+ *
+ * All graph traversal (impact, context, process detection) reads from
+ * this table after ingestion completes.
+ *
+ * Source and target reference nexus_nodes.id. They are soft FKs —
+ * unresolved targets (e.g., external packages) are stored as raw specifiers.
+ *
+ * @task T529
+ */
+export const nexusRelations = sqliteTable('nexus_relations', {
+    /** UUID v4 row identifier. */
+    id: text('id').primaryKey(),
+    /** Foreign key to project_registry.project_id. */
+    projectId: text('project_id').notNull(),
+    /** Source node ID (nexus_nodes.id). */
+    sourceId: text('source_id').notNull(),
+    /** Target node ID (nexus_nodes.id) or raw module specifier for
+     *  unresolved imports. Example: `@cleocode/contracts` or
+     *  `src/core/parser.ts::parseFile`. */
+    targetId: text('target_id').notNull(),
+    /** Semantic relation type. */
+    type: text('type', { enum: NEXUS_RELATION_TYPES }).notNull(),
+    /** Extractor confidence (0.0 to 1.0). */
+    confidence: real('confidence').notNull(),
+    /** Human-readable note explaining why this relation was emitted. */
+    reason: text('reason'),
+    /** Step index within an execution flow (for step_in_process relations). */
+    step: integer('step'),
+    /** ISO 8601 timestamp when this relation was last indexed. */
+    indexedAt: text('indexed_at').notNull().default(sql `(datetime('now'))`),
+}, (table) => [
+    index('idx_nexus_relations_project').on(table.projectId),
+    index('idx_nexus_relations_source').on(table.sourceId),
+    index('idx_nexus_relations_target').on(table.targetId),
+    index('idx_nexus_relations_type').on(table.type),
+    index('idx_nexus_relations_project_type').on(table.projectId, table.type),
+    index('idx_nexus_relations_source_type').on(table.sourceId, table.type),
+    index('idx_nexus_relations_target_type').on(table.targetId, table.type),
+    index('idx_nexus_relations_confidence').on(table.confidence),
+]);
+//# sourceMappingURL=nexus-schema.js.map

package/dist/store/nexus-schema.js.map

@@ -0,0 +1 @@
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package/dist/store/nexus-sqlite.js

@@ -0,0 +1,242 @@
+/**
+ * SQLite store for nexus.db via drizzle-orm/node-sqlite + node:sqlite (DatabaseSync).
+ *
+ * Separate database from tasks.db and brain.db for cross-project registry
+ * and audit infrastructure. Follows the same singleton + WAL + migration
+ * pattern as brain-sqlite.ts.
+ *
+ * nexus.db lives in ~/.cleo/ (global home) rather than per-project .cleo/,
+ * since it stores cross-project data.
+ *
+ * @task T5365
+ */
+import { copyFileSync, existsSync, mkdirSync } from 'node:fs';
+import { dirname, join } from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { readMigrationFiles } from 'drizzle-orm/migrator';
+import { drizzle } from 'drizzle-orm/node-sqlite';
+import { migrate } from 'drizzle-orm/node-sqlite/migrator';
+import { getCleoHome } from '../paths.js';
+import * as nexusSchema from './nexus-schema.js';
+import { isSqliteBusy, openNativeDatabase } from './sqlite.js';
+/** Database file name within ~/.cleo/ directory. */
+const DB_FILENAME = 'nexus.db';
+/** Schema version for newly created nexus databases. Single source of truth. */
+export const NEXUS_SCHEMA_VERSION = '1.0.0';
+/** Singleton state for lazy initialization. */
+let _nexusDb = null;
+let _nexusNativeDb = null;
+let _nexusDbPath = null;
+/** Guard against concurrent initialization (async migration). */
+let _nexusInitPromise = null;
+/**
+ * Returns the global-tier nexus.db path. ALWAYS under `getCleoHome()`.
+ *
+ * nexus.db is a cross-project registry and must live in the global CLEO
+ * home directory (`~/.local/share/cleo/` on Linux via XDG). It is NEVER
+ * written to a per-project `.cleo/` directory.
+ *
+ * @task T307
+ * @epic T299
+ * @why ADR-036 §Decision/Global-Tier: nexus.db is global-only. This guard
+ *   throws immediately if path resolution ever drifts outside getCleoHome(),
+ *   preventing silent creation of project-tier stray nexus.db files.
+ * @throws {Error} If the resolved path is not under `getCleoHome()` — this
+ *   indicates a code path that bypasses canonical path resolution and is a
+ *   bug that must be fixed rather than silently tolerated.
+ */
+export function getNexusDbPath() {
+    const cleoHome = getCleoHome();
+    const nexusPath = join(cleoHome, DB_FILENAME);
+    // Guard: the resolved path MUST be under the global tier.
+    // Under normal operation this invariant is always satisfied because we
+    // build nexusPath from cleoHome above. The assertion catches hypothetical
+    // future regressions where getCleoHome() is monkey-patched or join()
+    // produces an unexpected result on exotic platforms.
+    if (!nexusPath.startsWith(cleoHome)) {
+        throw new Error(`BUG: getNexusDbPath() resolved to "${nexusPath}" which is NOT under ` +
+            `getCleoHome() ("${cleoHome}"). nexus.db is global-only per ADR-036. ` +
+            `This indicates a code path that bypasses canonical path resolution — ` +
+            `fix the caller, do not suppress this error.`);
+    }
+    return nexusPath;
+}
+/**
+ * Resolve the path to the drizzle-nexus migrations folder.
+ * Works from both src/ (dev via tsx) and dist/ (compiled via esbuild bundle).
+ *
+ * - Source layout: __dirname = src/store/ → need ../../migrations/drizzle-nexus
+ * - Bundled layout: __dirname = dist/     → need ../migrations/drizzle-nexus
+ */
+export function resolveNexusMigrationsFolder() {
+    const __filename = fileURLToPath(import.meta.url);
+    const __dirname = dirname(__filename);
+    const isBundled = __dirname.endsWith('/dist') || __dirname.endsWith('\\dist');
+    const pkgRoot = isBundled ? join(__dirname, '..') : join(__dirname, '..', '..');
+    return join(pkgRoot, 'migrations', 'drizzle-nexus');
+}
+/**
+ * Check whether a table exists in the SQLite database.
+ */
+function tableExists(nativeDb, tableName) {
+    const result = nativeDb
+        .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name=?")
+        .get(tableName);
+    return !!result;
+}
+/**
+ * Run drizzle migrations to create/update nexus.db tables.
+ *
+ * Uses IMMEDIATE transactions to prevent concurrent migration races.
+ * Follows the same pattern as brain-sqlite.ts runBrainMigrations().
+ *
+ * @task T5365
+ */
+function runNexusMigrations(nativeDb, db) {
+    const migrationsFolder = resolveNexusMigrationsFolder();
+    // If existing DB with pending migrations, create safety backup (cleo compat)
+    if (tableExists(nativeDb, 'project_registry') && _nexusDbPath) {
+        const backupPath = _nexusDbPath.replace(/\.db$/, '-pre-cleo.db.bak');
+        if (!existsSync(backupPath)) {
+            try {
+                copyFileSync(_nexusDbPath, backupPath);
+            }
+            catch {
+                /* non-fatal */
+            }
+        }
+    }
+    // Bootstrap existing databases that predate drizzle migrations.
+    // Mark baseline migration as already applied if tables exist but
+    // __drizzle_migrations doesn't.
+    if (tableExists(nativeDb, 'project_registry') && !tableExists(nativeDb, '__drizzle_migrations')) {
+        const migrations = readMigrationFiles({ migrationsFolder });
+        const baseline = migrations[0];
+        if (baseline) {
+            nativeDb
+                .prepare(`CREATE TABLE IF NOT EXISTS "__drizzle_migrations" (id SERIAL PRIMARY KEY, hash text NOT NULL, created_at numeric)`)
+                .run();
+            nativeDb
+                .prepare(`INSERT INTO "__drizzle_migrations" ("hash", "created_at") VALUES ('${baseline.hash}', ${baseline.folderMillis})`)
+                .run();
+        }
+    }
+    // Run pending migrations via drizzle-orm/node-sqlite/migrator (synchronous).
+    const MAX_RETRIES = 5;
+    const BASE_DELAY_MS = 100;
+    const MAX_DELAY_MS = 2000;
+    let lastError;
+    for (let attempt = 1; attempt <= MAX_RETRIES; attempt++) {
+        try {
+            migrate(db, { migrationsFolder });
+            return;
+        }
+        catch (err) {
+            if (!isSqliteBusy(err) || attempt === MAX_RETRIES)
+                throw err;
+            lastError = err;
+            const delay = Math.min(BASE_DELAY_MS * 2 ** (attempt - 1) * (1 + Math.random() * 0.5), MAX_DELAY_MS);
+            Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, Math.round(delay));
+        }
+    }
+    /* c8 ignore next */
+    throw lastError;
+}
+/**
+ * Initialize the nexus.db SQLite database (lazy, singleton).
+ * Creates the database file and tables if they don't exist.
+ * Returns the drizzle ORM instance (async via sqlite-proxy).
+ *
+ * Uses a promise guard so concurrent callers wait for the same
+ * initialization to complete (migrations are async).
+ */
+export async function getNexusDb() {
+    const requestedPath = getNexusDbPath();
+    // If singleton exists but points to different path, reset it
+    if (_nexusDb && _nexusDbPath !== requestedPath) {
+        resetNexusDbState();
+    }
+    if (_nexusDb)
+        return _nexusDb;
+    // If already initializing, wait for the in-flight init
+    if (_nexusInitPromise)
+        return _nexusInitPromise;
+    _nexusInitPromise = (async () => {
+        const dbPath = requestedPath;
+        _nexusDbPath = dbPath;
+        // Ensure directory exists
+        mkdirSync(dirname(dbPath), { recursive: true });
+        // Open file-backed SQLite via node:sqlite with WAL mode.
+        const nativeDb = openNativeDatabase(dbPath);
+        _nexusNativeDb = nativeDb;
+        // Create drizzle ORM wrapper via node-sqlite
+        const db = drizzle({ client: nativeDb, schema: nexusSchema });
+        // Run drizzle migrations (creates/updates tables)
+        runNexusMigrations(nativeDb, db);
+        // Seed schema version for new databases (no-op if already set)
+        nativeDb
+            .prepare(`INSERT OR IGNORE INTO nexus_schema_meta (key, value) VALUES ('schemaVersion', '${NEXUS_SCHEMA_VERSION}')`)
+            .run();
+        // Set singleton only after migrations complete
+        _nexusDb = db;
+        return db;
+    })();
+    try {
+        return await _nexusInitPromise;
+    }
+    finally {
+        _nexusInitPromise = null;
+    }
+}
+/**
+ * Close the nexus.db database connection and release resources.
+ */
+export function closeNexusDb() {
+    if (_nexusNativeDb) {
+        try {
+            if (_nexusNativeDb.isOpen) {
+                _nexusNativeDb.close();
+            }
+        }
+        catch {
+            // Ignore close errors
+        }
+        _nexusNativeDb = null;
+    }
+    _nexusDb = null;
+    _nexusDbPath = null;
+}
+/**
+ * Reset nexus.db singleton state without saving.
+ * Used during tests or when database file is recreated.
+ * Safe to call multiple times.
+ */
+export function resetNexusDbState() {
+    if (_nexusNativeDb) {
+        try {
+            if (_nexusNativeDb.isOpen) {
+                _nexusNativeDb.close();
+            }
+        }
+        catch {
+            // Ignore close errors
+        }
+        _nexusNativeDb = null;
+    }
+    _nexusDb = null;
+    _nexusDbPath = null;
+    _nexusInitPromise = null;
+}
+/**
+ * Get the underlying node:sqlite DatabaseSync instance for nexus.db.
+ * Useful for direct PRAGMA calls or raw SQL operations.
+ * Returns null if the database hasn't been initialized.
+ */
+export function getNexusNativeDb() {
+    return _nexusNativeDb;
+}
+/**
+ * Re-export nexus schema for external use.
+ */
+export { nexusSchema };
+//# sourceMappingURL=nexus-sqlite.js.map

package/dist/store/nexus-sqlite.js.map

@@ -0,0 +1 @@
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package/dist/store/nexus-validation-schemas.js

@@ -0,0 +1,40 @@
+/**
+ * Drizzle-derived Zod validation schemas for CLEO nexus.db tables.
+ *
+ * Uses `drizzle-orm/zod` to generate insert/select validation schemas
+ * directly from Drizzle table definitions in `./nexus-schema.ts`.
+ *
+ * Domain types (NexusProject, NexusRegistryFile, etc.) live in
+ * `../nexus/registry.ts` as plain interfaces — they have different
+ * field names from the DB rows, so they cannot be derived from
+ * createSelectSchema. The row-to-domain mapping is handled by
+ * `rowToProject()` in `../nexus/registry.ts`.
+ *
+ * @module nexus-validation-schemas
+ */
+import { createSchemaFactory } from 'drizzle-orm/zod';
+import { z } from 'zod';
+// Use factory to bind our zod instance — ensures drizzle-orm/zod uses
+// the same z we use everywhere. The type assertion is needed because
+// drizzle-orm beta.18's CoerceOptions type doesn't match zod's coerce
+// namespace shape (works correctly at runtime).
+const { createInsertSchema, createSelectSchema } = createSchemaFactory(z);
+import { nexusAuditLog, nexusSchemaMeta, projectRegistry } from './nexus-schema.js';
+// === PROJECT REGISTRY ===
+export const insertProjectRegistrySchema = createInsertSchema(projectRegistry, {
+    projectId: (s) => s.min(1),
+    projectHash: (s) => s.regex(/^[a-f0-9]{12}$/),
+    projectPath: (s) => s.min(1),
+    name: (s) => s.min(1).max(64),
+});
+export const selectProjectRegistrySchema = createSelectSchema(projectRegistry);
+// === NEXUS AUDIT LOG ===
+export const insertNexusAuditLogSchema = createInsertSchema(nexusAuditLog, {
+    id: (s) => s.min(1),
+    action: (s) => s.min(1).max(100),
+});
+export const selectNexusAuditLogSchema = createSelectSchema(nexusAuditLog);
+// === NEXUS SCHEMA META ===
+export const insertNexusSchemaMetaSchema = createInsertSchema(nexusSchemaMeta);
+export const selectNexusSchemaMetaSchema = createSelectSchema(nexusSchemaMeta);
+//# sourceMappingURL=nexus-validation-schemas.js.map

package/dist/store/nexus-validation-schemas.js.map

@@ -0,0 +1 @@
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package/dist/store/parsers.js

@@ -0,0 +1,37 @@
+/**
+ * Shared JSON parsing helpers for SQLite store modules.
+ *
+ * Eliminates duplication across sqlite-data-accessor.ts, task-store.ts,
+ * and session-store.ts.
+ */
+/**
+ * Parse a JSON string, returning undefined on null/undefined input or parse error.
+ */
+export function safeParseJson(str) {
+    if (!str)
+        return undefined;
+    try {
+        return JSON.parse(str);
+    }
+    catch {
+        return undefined;
+    }
+}
+/**
+ * Parse a JSON string expected to contain an array.
+ * Returns undefined for null/undefined input, empty arrays, or parse errors.
+ */
+export function safeParseJsonArray(str) {
+    if (!str)
+        return undefined;
+    try {
+        const arr = JSON.parse(str);
+        if (Array.isArray(arr) && arr.length === 0)
+            return undefined;
+        return arr;
+    }
+    catch {
+        return undefined;
+    }
+}
+//# sourceMappingURL=parsers.js.map

package/dist/store/parsers.js.map

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