code-auditor-mcp 4.1.1 → 5.0.2

package/dist/codeIndexDB.d.ts

@@ -1,18 +1,41 @@
 /**
  * Code Index Database using SQLite (better-sqlite3) + FTS5
  * Replaces LokiJS + FlexSearch with durable, transactional storage.
+ *
+ * `CodeIndexDB` is the connection owner and transaction boundary, plus the
+ * cross-concern orchestrators (sync, diff detection, churn/hotspot/convention
+ * mining). Each storage concern — functions, search, coverage, dependency
+ * graph, schema usage, whitelist, audit results, analyzer configs, code maps,
+ * project tasks, meta, provenance, inferred receivers, conventions, raw SQL —
+ * lives in its own module under `codeIndex/` and is exposed as a public field.
  */
+import { DB_BUSY_TIMEOUT_MS } from './sqlite/driver.js';
 import type { SqliteDatabase } from './sqlite/types.js';
-import type { CompleteProjectTaskResult, CreateProjectTaskInput, ListProjectTasksOptions, ListProjectTasksTreeNode, ProjectTask, ProjectTaskDeleteMode } from './types/projectTask.js';
-import { EnhancedFunctionMetadata, FunctionMetadata, SearchResult, SearchOptions, SchemaDefinition, SchemaIndexMetadata, SchemaUsage } from './types.js';
-import { WhitelistEntry, WhitelistType, WhitelistStatus, WhitelistSuggestion } from './types/whitelist.js';
-export declare const DB_BUSY_TIMEOUT_MS = 30000;
-/** Reject a value that is not a plain SQL identifier. Table and column names are
- *  interpolated into SQL (SQLite cannot parameterize identifiers), so a value that
- *  fails this check is a would-be injection surface and is refused, never run. */
-export declare function assertSqlIdentifier(name: string, context: string): void;
-/** Escape regex metacharacters so a string matches itself literally. */
-export declare function escapeRegExpLiteral(s: string): string;
+import type { EnhancedFunctionMetadata, FunctionMetadata, IndexHandle, SearchResult, SearchOptions } from './types.js';
+import { CoverageIndex } from './codeIndex/coverage.js';
+import { DependencyGraphIndex } from './codeIndex/dependencyGraph.js';
+import { FunctionIndex } from './codeIndex/functionIndex.js';
+import { SearchIndex } from './codeIndex/search.js';
+import { SchemaMigrations } from './codeIndex/migrations.js';
+import { MetaStore } from './codeIndex/meta.js';
+import { ProvenanceStore } from './codeIndex/provenance.js';
+import { InferredReceiversStore } from './codeIndex/inferredReceivers.js';
+import { CodeMapIndex } from './codeIndex/codeMap.js';
+import { AnalyzerConfigIndex } from './codeIndex/analyzerConfig.js';
+import { AuditResultsIndex } from './codeIndex/auditResults.js';
+import { WhitelistIndex } from './codeIndex/whitelist.js';
+import { SchemaIndex } from './codeIndex/schema.js';
+import { ProjectTasksIndex } from './codeIndex/projectTasks.js';
+import { ConventionsIndex } from './codeIndex/conventions.js';
+import { RawSqlIndex } from './codeIndex/rawSql.js';
+export { assertSqlIdentifier, escapeRegExpLiteral } from './codeIndex/shared.js';
+export { DB_BUSY_TIMEOUT_MS };
+/**
+ * SQLite-backed code index for a single project. Connection owner and
+ * transaction boundary; storage concerns live on the public module fields
+ * (`functionIndex`, `search`, `coverage`, `graph`, `whitelist`, `schema`,
+ * `projectTasks`, `meta`, …) and cross-concern orchestration stays here.
+ */
 export declare class CodeIndexDB {
     private static instance;
     /** Subclasses (e.g. EnhancedCodeIndexDB) need access for extra tables without `as any`. */
@@ -26,26 +49,46 @@ export declare class CodeIndexDB {
      *  *cause* (e.g. missing better-sqlite3 binding) instead of the generic
      *  "Database not initialized". Cleared on success and on close(). */
     private initFailure;
-    private functionsAdapter;
-    private whitelistAdapter;
-    private auditResultsAdapter;
-    private analyzerConfigAdapter;
-    private codeMapAdapter;
-    private schemaAdapter;
-    private schemaUsageAdapter;
-    private tasksAdapter;
-    private conventionsAdapter;
-    private fileChurnAdapter;
-    private functionChurnAdapter;
-    private pairHistoryAdapter;
-    private hotspotScoresAdapter;
-    private graphCacheAdapter;
-    private taskRepository;
-    private stmts;
+    migrations: SchemaMigrations;
+    functionIndex: FunctionIndex;
+    search: SearchIndex;
+    coverage: CoverageIndex;
+    graph: DependencyGraphIndex;
+    meta: MetaStore;
+    provenance: ProvenanceStore;
+    inferredReceivers: InferredReceiversStore;
+    codeMap: CodeMapIndex;
+    analyzerConfig: AnalyzerConfigIndex;
+    auditResults: AuditResultsIndex;
+    whitelist: WhitelistIndex;
+    schema: SchemaIndex;
+    projectTasks: ProjectTasksIndex;
+    conventions: ConventionsIndex;
+    rawSql: RawSqlIndex;
+    /**
+     * Read-only facade analyzers consume — the raw-SQL, meta, and coverage
+     * concerns composed into the `IndexHandle` contract. Built once at
+     * initialization; a plain object field (not delegator methods), so it adds
+     * nothing to `solid/class-size`.
+     */
+    indexHandle: IndexHandle;
     private static readonly SCHEMA_VERSION;
+    /**
+     * Create an index handle for the given SQLite file (in-memory by default).
+     *
+     * @param dbPath - Path to the SQLite database file, or ':memory:'.
+     */
     constructor(dbPath?: string);
     /** The project root this singleton was opened for (used for mismatch detection). */
     private static currentProjectRoot;
+    /**
+     * Return the process-wide singleton, reopening the store when the requested
+     * path differs from the one currently open.
+     *
+     * @param dbPath - Optional explicit database file path.
+     * @param projectRoot - The project root the store is scoped to.
+     * @returns The singleton index instance.
+     */
     static getInstance(dbPath?: string, projectRoot?: string): CodeIndexDB;
     /** Reset the singleton — used by tests that need a fresh in-memory instance. */
     static resetInstance(): void;
@@ -55,31 +98,26 @@ export declare class CodeIndexDB {
      * opened, without re-resolving against cwd and flipping the singleton away.
      */
     static get currentProject(): string | undefined;
+    /**
+     * Initialize the database schema and adapters once, memoized via a shared
+     * promise so concurrent callers await the same initialization.
+     *
+     * @returns A promise that resolves once initialization completes.
+     */
     initialize(): Promise<void>;
     private initializeInternal;
-    private runMigrations;
-    private createSchema;
-    private maybeMigrateFromLokiJS;
     private ensureInitialized;
-    private rowToFunction;
-    private functionToRow;
-    registerFunction(func: FunctionMetadata | EnhancedFunctionMetadata): Promise<void>;
-    registerFunctions(functions: (FunctionMetadata | EnhancedFunctionMetadata)[]): Promise<{
-        success: boolean;
-        registered: number;
-        failed: number;
-        errors?: Array<{
-            function: string;
-            error: string;
-        }>;
-    }>;
     /**
-     * Upsert/remove one file's function rows. Runs inside the caller's
-     * transaction (no nested `db.transaction` here) so a batch sync can wrap many
-     * files in a single write transaction.
+     * Upsert one file's functions and remove rows that no longer exist, then
+     * rebuild the dependency graph for that file.
+     *
+     * @param filePath - The file whose functions are being synced.
+     * @param currentFunctions - The functions currently present in the file.
+     * @param fileHash - Optional file-level content hash stamped onto each written
+     *   row for diff detection.
+     * @returns Counts of added, updated, and removed rows.
      */
-    private syncFileIndexRow;
-    syncFileIndex(filePath: string, currentFunctions: (FunctionMetadata | EnhancedFunctionMetadata)[]): Promise<{
+    syncFileIndex(filePath: string, currentFunctions: (FunctionMetadata | EnhancedFunctionMetadata)[], fileHash?: string): Promise<{
         added: number;
         updated: number;
         removed: number;
@@ -91,52 +129,51 @@ export declare class CodeIndexDB {
      * one transaction plus one dependency-graph rebuild per file, and the
      * rebuild's un-scoped `SELECT` made that O(files × functions). Collapsing it
      * to one transaction is Amendment B2.
+     *
+     * @param entries - The per-file sync entries (path plus current functions).
+     * @returns Counts of added, updated, and removed rows across all files.
      */
     syncFileIndexBatch(entries: Array<{
         filePath: string;
         currentFunctions: (FunctionMetadata | EnhancedFunctionMetadata)[];
+        fileHash?: string;
     }>): Promise<{
         added: number;
         updated: number;
         removed: number;
     }>;
-    updateDependencyGraph(filePath?: string): Promise<void>;
-    getTransitiveDependencies(functionName: string, maxDepth?: number): Promise<Array<{
-        name: string;
-        depth: number;
-    }>>;
-    getTransitiveCallers(functionName: string, maxDepth?: number): Promise<Array<{
-        name: string;
-        depth: number;
-    }>>;
-    detectCircularDependencies(): Promise<Array<string[]>>;
-    calculateDependencyDepths(): Promise<void>;
-    searchFunctions(options: SearchOptions): Promise<SearchResult>;
-    private executeCompiledSearch;
-    private rowToFunctionDoc;
-    findDefinition(name: string, filePath?: string): Promise<EnhancedFunctionMetadata | null>;
-    getAllFunctions(): Promise<EnhancedFunctionMetadata[]>;
-    /** Row count of the `functions` table — for callers that only need `.length`. */
-    getFunctionCount(): Promise<number>;
-    getStats(): Promise<{
-        totalFunctions: number;
-        languages: Record<string, number>;
-        topDependencies: Array<{
-            name: string;
-            count: number;
-        }>;
-        filesIndexed: number;
-        lastUpdated: Date;
-    }>;
-    /** Get graph statistics — delegates to graph/callGraph.ts (Spec 14 R1). */
-    getGraphStats(): import('./types.js').GraphStats;
+    /**
+     * Delete all index data while preserving project tasks, configs, whitelist,
+     * and ledger rows.
+     *
+     * @returns A promise that resolves once the index is cleared.
+     */
     clearIndex(): Promise<void>;
+    /**
+     * Close the database handle and release resources, if initialized.
+     *
+     * @returns A promise that resolves once the handle is closed.
+     */
     close(): Promise<void>;
+    /**
+     * Re-scan a single file and reconcile its indexed functions, removing rows
+     * when the file no longer exists.
+     *
+     * @param filePath - The file to synchronize.
+     * @returns Counts of added, updated, and removed rows (null on scan error).
+     */
     synchronizeFile(filePath: string): Promise<{
         added: number;
         updated: number;
         removed: number;
     } | null>;
+    /**
+     * Remove stale function rows whose files are deleted or no longer part of
+     * the discovery set.
+     *
+     * @param projectRoot - Optional project root to reconcile against.
+     * @returns Scan counts, removed rows, and per-file errors.
+     */
     bulkCleanup(projectRoot?: string): Promise<{
         scannedCount: number;
         removedCount: number;
@@ -146,6 +183,14 @@ export declare class CodeIndexDB {
             error: string;
         }>;
     }>;
+    /**
+     * Re-scan the whole project (or the already-indexed files) and reconcile the
+     * index, reporting aggregate counts.
+     *
+     * @param projectRoot - Optional project root to discover files from.
+     * @param progressCallback - Optional per-file progress callback.
+     * @returns Aggregate sync counts and errors.
+     */
     deepSync(projectRoot?: string, progressCallback?: (progress: {
         current: number;
         total: number;
@@ -167,6 +212,9 @@ export declare class CodeIndexDB {
      *
      * Returns the list of changed/new function metadata for scoped analysis,
      * and the set of file paths that were actually touched.
+     *
+     * @param filePaths - The file paths to re-parse and diff.
+     * @returns Changed and deleted functions, touched paths, and per-file errors.
      */
     detectChangedFunctions(filePaths: string[]): Promise<{
         changedFunctions: EnhancedFunctionMetadata[];
@@ -180,90 +228,18 @@ export declare class CodeIndexDB {
     /**
      * Given a project root, detect all indexed files whose mtime is newer than
      * the stored last_modified timestamp. Returns file paths for further processing.
+     *
+     * @param projectRoot - The project root to scan.
+     * @returns The file paths whose mtime is newer than the stored timestamp.
      */
     detectModifiedFiles(projectRoot: string): Promise<string[]>;
     /**
-     * Get content hashes for a set of file paths. Returns a map:
-     * file_path → { name → content_hash }
-     */
-    getContentHashesForFiles(filePaths: string[]): Map<string, Map<string, string>>;
-    private mergeFilters;
-    private applyFilters;
-    private excludeTermsFromResults;
-    private initializeDefaultWhitelists;
-    getWhitelist(type?: WhitelistType, status?: WhitelistStatus): Promise<WhitelistEntry[]>;
-    addWhitelistEntry(entry: Omit<WhitelistEntry, 'id' | 'addedAt'>): Promise<WhitelistEntry>;
-    updateWhitelistStatus(name: string, status: WhitelistStatus): Promise<void>;
-    isWhitelisted(name: string, type: WhitelistType): boolean;
-    detectWhitelistCandidates(): Promise<WhitelistSuggestion[]>;
-    storeAuditResults(auditResult: any, projectPath: string): Promise<string>;
-    getAuditResults(auditId: string): Promise<any | null>;
-    getMostRecentAuditResults(projectPath?: string, resultScope?: 'full' | 'scoped'): Promise<any | null>;
-    hasOpenTaskByFingerprint(fingerprint: string | null | undefined): boolean;
-    private cleanupExpiredAudits;
-    storeAnalyzerConfig(analyzerName: string, config: Record<string, any>, options?: {
-        projectPath?: string;
-        isGlobal?: boolean;
-        metadata?: any;
-    }): Promise<string>;
-    getAnalyzerConfig(analyzerName: string, projectPath?: string): Promise<Record<string, any> | null>;
-    getAllAnalyzerConfigs(projectPath?: string): Promise<Record<string, any>>;
-    deleteAnalyzerConfig(analyzerName: string, options?: {
-        projectPath?: string;
-        isGlobal?: boolean;
-    }): Promise<boolean>;
-    resetAnalyzerConfigs(projectPath?: string): Promise<void>;
-    storeCodeMapSection(mapId: string, sectionType: string, content: string, metadata?: any): Promise<void>;
-    getCodeMapSection(mapId: string, sectionType: string): Promise<{
-        content: string;
-        metadata: any;
-    } | null>;
-    listCodeMapSections(mapId: string): Promise<Array<{
-        sectionType: string;
-        size: number;
-        timestamp: Date;
-    }>>;
-    clearOldCodeMaps(olderThanHours?: number): Promise<number>;
-    deleteCodeMap(mapId: string): Promise<number>;
-    storeSchema(schema: SchemaDefinition): Promise<string>;
-    getSchema(schemaId: string): Promise<SchemaDefinition | null>;
-    getAllSchemas(): Promise<Array<{
-        schemaId: string;
-        metadata: SchemaIndexMetadata;
-        schema: SchemaDefinition;
-    }>>;
-    deleteSchema(schemaId: string): Promise<boolean>;
-    recordSchemaUsage(usage: SchemaUsage, schemaId?: string): Promise<void>;
-    /**
-     * Clear all schema_usage entries for a given file path.
-     * Used for idempotent per-file writes during indexing — stale entries
-     * from a previous scan are removed before fresh references are inserted.
+     * Search functions and optionally annotate results with schema usage context.
+     *
+     * @param options - Search options, including includeSchemaUsage.
+     * @returns The search result, with schema context when requested.
      */
-    clearSchemaUsageForFile(filePath: string): void;
-    getSchemaUsage(options?: {
-        schemaId?: string;
-        tableName?: string;
-        filePath?: string;
-        functionName?: string;
-        usageType?: string;
-    }): Promise<SchemaUsage[]>;
-    findFunctionsUsingTable(tableName: string): Promise<Array<{
-        functionName: string;
-        filePath: string;
-        usageType: string;
-        line: number;
-    }>>;
-    getSchemaStats(): Promise<{
-        totalSchemas: number;
-        totalTables: number;
-        totalUsagePatterns: number;
-        mostUsedTables: Array<{
-            tableName: string;
-            usageCount: number;
-        }>;
-        usageByType: Record<string, number>;
-    }>;
-    searchWithSchemaContext(query: string, options?: SearchOptions & {
+    searchWithSchemaContext(options?: SearchOptions & {
         includeSchemaUsage?: boolean;
     }): Promise<SearchResult & {
         schemaContext?: Array<{
@@ -271,120 +247,5 @@ export declare class CodeIndexDB {
             usageType: string;
         }>;
     }>;
-    private getTaskRepository;
-    createProjectTask(input: CreateProjectTaskInput): Promise<ProjectTask>;
-    getProjectTask(taskId: string): Promise<ProjectTask | null>;
-    listProjectTasks(projectPath: string, options?: ListProjectTasksOptions): Promise<ProjectTask[]>;
-    listProjectTasksTree(projectPath: string, options?: Omit<ListProjectTasksOptions, 'parentTaskId' | 'hasChildren'>): Promise<ListProjectTasksTreeNode[]>;
-    listActionableProjectTasks(projectPath: string, options?: Omit<ListProjectTasksOptions, 'actionableOnly'>): Promise<ProjectTask[]>;
-    completeProjectTask(taskId: string): Promise<CompleteProjectTaskResult | null>;
-    updateProjectTask(taskId: string, patch: unknown): Promise<ProjectTask | null>;
-    deleteProjectTask(taskId: string, mode?: ProjectTaskDeleteMode): Promise<boolean>;
-    /** Upsert a key-value pair in the meta table. */
-    setMeta(key: string, value: string): void;
-    /** Retrieve a value from the meta table, or null if absent. */
-    getMeta(key: string): string | null;
-    /** Store per-file provenance context in the meta table. */
-    storeFileProvenance(filePath: string, provenanceData: {
-        dbProvenanced: Array<{
-            identifier: string;
-            reason: string;
-            source: string;
-            chain?: string[];
-        }>;
-        validatorProvenanced: Array<{
-            identifier: string;
-            reason: string;
-            source: string;
-            chain?: string[];
-        }>;
-    }): void;
-    /** Retrieve per-file provenance context, or null if not stored. */
-    getFileProvenance(filePath: string): {
-        dbProvenanced: Array<{
-            identifier: string;
-            reason: string;
-            source: string;
-            chain?: string[];
-        }>;
-        validatorProvenanced: Array<{
-            identifier: string;
-            reason: string;
-            source: string;
-            chain?: string[];
-        }>;
-    } | null;
-    /** Store the inferred receiver set as a meta record. */
-    storeInferredReceivers(inferred: Array<{
-        identifier: string;
-        file: string;
-        reason: string;
-    }>): void;
-    /** Retrieve the inferred receiver set, or null if not stored. */
-    getInferredReceivers(): Array<{
-        identifier: string;
-        file: string;
-        reason: string;
-    }> | null;
-    /** Import coverage entries, replacing any existing data for the given basis. */
-    importCoverageData(entries: Array<{
-        functionName: string;
-        filePath: string;
-        lineNumber: number;
-        basis: 'static-reach' | 'measured';
-        covered: boolean;
-        source?: string;
-    }>): void;
-    /** Get all coverage entries for a given basis. */
-    getCoverageByBasis(basis: 'static-reach' | 'measured'): Array<{
-        functionName: string;
-        filePath: string;
-        lineNumber: number;
-        basis: string;
-        covered: boolean;
-        source: string | null;
-        importedAt: string | null;
-    }>;
-    /** Clear coverage data, optionally scoped to a single basis. */
-    clearCoverageData(basis?: 'static-reach' | 'measured'): void;
-    /** Check if measured coverage data is stale (older than the last full sync). */
-    isCoverageStale(): boolean;
-    /** Get coverage rate by risk decile for the coverage report. */
-    getCoverageByRiskDecile(decileCount?: number): Array<{
-        decile: number;
-        covered: number;
-        total: number;
-        rate: number;
-    }>;
-    /** Get untested functions in the top risk decile. */
-    getUntestedTopDecile(topDecile?: number): Array<{
-        functionName: string;
-        filePath: string;
-        lineNumber: number;
-        riskScore: number;
-        basis: string;
-    }>;
-    /** Execute a parameterized query and return all rows. */
-    query(sql: string, params?: any[]): any[];
-    /** Count rows in a table, with optional WHERE clause. */
-    count(table: string, where?: string, params?: any[]): number;
-    /** Check if a table has any rows. */
-    tableHasRows(table: string): boolean;
-    /**
-     * Mine codebase conventions from the functions table and upsert into the
-     * conventions table. Content-hash-based skip: stored hash avoids re-mining
-     * when the function corpus hasn't changed since the last mine.
-     *
-     * Called both by deepSync() (after indexing) and by audit runs (so the
-     * conventions analyzer has data to query even without an explicit sync).
-     */
-    mineAllConventions(projectRoot?: string, getSource?: (filePath: string) => string | undefined): void;
-    /** Execute a DML statement (INSERT/UPDATE/DELETE) and return its result. */
-    run(sql: string, params?: unknown[]): {
-        changes: number;
-        lastInsertRowid: number | bigint;
-    };
-    /** Execute raw SQL (multi-statement) — for schema setup / bulk operations. */
-    exec(sql: string): void;
 }
 //# sourceMappingURL=codeIndexDB.d.ts.map

package/dist/codeIndexDB.d.ts.map

@@ -1 +1 @@
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