@colbymchenry/codegraph 0.9.7 → 0.9.9

package/dist/index.d.ts

@@ -0,0 +1,498 @@
+/**
+ * CodeGraph
+ *
+ * A local-first code intelligence system that builds a semantic
+ * knowledge graph from any codebase.
+ */
+import { Node, Edge, FileRecord, ExtractionResult, Subgraph, TraversalOptions, SearchOptions, SearchResult, Context, GraphStats, TaskInput, TaskContext, BuildContextOptions, FindRelevantContextOptions } from './types';
+import { IndexProgress, IndexResult, SyncResult } from './extraction';
+import { ResolutionResult } from './resolution';
+import { WatchOptions, PendingFile } from './sync';
+export * from './types';
+export { getDatabasePath, DatabaseConnection } from './db';
+export { QueryBuilder } from './db/queries';
+export { getCodeGraphDir, isInitialized, findNearestCodeGraphRoot, CODEGRAPH_DIR, } from './directory';
+export { IndexProgress, IndexResult, SyncResult } from './extraction';
+export { detectLanguage, isLanguageSupported, isGrammarLoaded, getSupportedLanguages, initGrammars, loadGrammarsForLanguages, loadAllGrammars } from './extraction';
+export { ResolutionResult } from './resolution';
+export { CodeGraphError, FileError, ParseError, DatabaseError, SearchError, VectorError, ConfigError, Logger, setLogger, getLogger, silentLogger, defaultLogger, } from './errors';
+export { Mutex, FileLock, processInBatches, debounce, throttle, MemoryMonitor } from './utils';
+export { FileWatcher, WatchOptions, PendingFile, LockUnavailableError } from './sync';
+export { MCPServer } from './mcp';
+/**
+ * Options for initializing a new CodeGraph project
+ */
+export interface InitOptions {
+    /** Whether to run initial indexing after init */
+    index?: boolean;
+    /** Progress callback for indexing */
+    onProgress?: (progress: IndexProgress) => void;
+}
+/**
+ * Options for opening an existing CodeGraph project
+ */
+export interface OpenOptions {
+    /** Whether to run sync if files have changed */
+    sync?: boolean;
+    /** Whether to run in read-only mode */
+    readOnly?: boolean;
+}
+/**
+ * Options for indexing
+ */
+export interface IndexOptions {
+    /** Progress callback */
+    onProgress?: (progress: IndexProgress) => void;
+    /** Abort signal for cancellation */
+    signal?: AbortSignal;
+    /** Enable verbose logging (worker lifecycle, memory, timeouts) */
+    verbose?: boolean;
+}
+/**
+ * Main CodeGraph class
+ *
+ * Provides the primary interface for interacting with the code knowledge graph.
+ */
+export declare class CodeGraph {
+    private db;
+    private queries;
+    private projectRoot;
+    private orchestrator;
+    private resolver;
+    private graphManager;
+    private traverser;
+    private contextBuilder;
+    private indexMutex;
+    private fileLock;
+    private watcher;
+    private constructor();
+    /**
+     * Initialize a new CodeGraph project
+     *
+     * Creates the .CodeGraph directory, database, and configuration.
+     *
+     * @param projectRoot - Path to the project root directory
+     * @param options - Initialization options
+     * @returns A new CodeGraph instance
+     */
+    static init(projectRoot: string, options?: InitOptions): Promise<CodeGraph>;
+    /**
+     * Initialize synchronously (without indexing)
+     */
+    static initSync(projectRoot: string): CodeGraph;
+    /**
+     * Open an existing CodeGraph project
+     *
+     * @param projectRoot - Path to the project root directory
+     * @param options - Open options
+     * @returns A CodeGraph instance
+     */
+    static open(projectRoot: string, options?: OpenOptions): Promise<CodeGraph>;
+    /**
+     * Open synchronously (without sync)
+     */
+    static openSync(projectRoot: string): CodeGraph;
+    /**
+     * Check if a directory has been initialized as a CodeGraph project
+     */
+    static isInitialized(projectRoot: string): boolean;
+    /**
+     * Close the CodeGraph instance and release resources
+     */
+    close(): void;
+    /**
+     * Get the project root directory
+     */
+    getProjectRoot(): string;
+    /**
+     * Index all files in the project
+     *
+     * Uses a mutex to prevent concurrent indexing operations.
+     */
+    indexAll(options?: IndexOptions): Promise<IndexResult>;
+    /**
+     * Index specific files
+     *
+     * Uses a mutex to prevent concurrent indexing operations.
+     */
+    indexFiles(filePaths: string[]): Promise<IndexResult>;
+    /**
+     * Sync with current file state (incremental update)
+     *
+     * Uses a mutex to prevent concurrent indexing operations.
+     */
+    sync(options?: IndexOptions): Promise<SyncResult>;
+    /**
+     * Check if an indexing operation is currently in progress
+     */
+    isIndexing(): boolean;
+    /**
+     * Start watching for file changes and auto-syncing.
+     *
+     * Uses native OS file events (FSEvents on macOS, inotify on Linux 19+,
+     * ReadDirectoryChangesW on Windows) with debouncing to avoid thrashing.
+     *
+     * @param options - Watch options (debounce delay, callbacks)
+     * @returns true if watching started successfully
+     */
+    watch(options?: WatchOptions): boolean;
+    /**
+     * Stop watching for file changes.
+     */
+    unwatch(): void;
+    /**
+     * Check if the file watcher is active.
+     */
+    isWatching(): boolean;
+    /**
+     * Files seen by the file watcher since the last successful sync —
+     * the per-file "stale" signal MCP tools attach to responses so an agent
+     * can fall back to {@link Read} for just the affected file without
+     * waiting for a debounced sync to complete (issue #403).
+     *
+     * Returns an empty list when the watcher isn't active, or no events have
+     * arrived. Each entry includes `firstSeenMs` and `lastSeenMs` (wall-clock
+     * `Date.now()` values) so callers can render "edited Nms ago", plus an
+     * `indexing` flag indicating whether the in-flight sync (if any) will
+     * absorb that file.
+     */
+    getPendingFiles(): PendingFile[];
+    /**
+     * Resolves once the file watcher has finished its initial chokidar scan.
+     * Useful for tests that need a deterministic boundary before asserting on
+     * `getPendingFiles()`. Resolves immediately when no watcher is active.
+     */
+    waitUntilWatcherReady(timeoutMs?: number): Promise<void>;
+    /**
+     * Get files that have changed since last index
+     */
+    getChangedFiles(): {
+        added: string[];
+        modified: string[];
+        removed: string[];
+    };
+    /**
+     * Extract nodes and edges from source code (without storing)
+     */
+    extractFromSource(filePath: string, source: string): ExtractionResult;
+    /**
+     * Resolve unresolved references and create edges
+     *
+     * This method takes unresolved references from extraction and attempts
+     * to resolve them using multiple strategies:
+     * - Framework-specific patterns (React, Express, Laravel)
+     * - Import-based resolution
+     * - Name-based symbol matching
+     */
+    resolveReferences(onProgress?: (current: number, total: number) => void): ResolutionResult;
+    /**
+     * Resolve references in batches to keep memory bounded on large codebases.
+     * Processes chunks of unresolved refs, persisting results after each batch.
+     */
+    resolveReferencesBatched(onProgress?: (current: number, total: number) => void): Promise<ResolutionResult>;
+    /**
+     * Get detected frameworks in the project
+     */
+    getDetectedFrameworks(): string[];
+    /**
+     * Re-initialize the resolver (useful after adding new files)
+     */
+    reinitializeResolver(): void;
+    /**
+     * Get statistics about the knowledge graph
+     */
+    getStats(): GraphStats;
+    /**
+     * Active SQLite backend for this project's connection (`node-sqlite` — Node's
+     * built-in real-SQLite module). Surfaced via `codegraph status` and the
+     * `codegraph_status` MCP tool alongside the effective journal mode.
+     */
+    getBackend(): import('./db').SqliteBackend;
+    /**
+     * The journal mode actually in effect ('wal', 'delete', …). 'wal' means
+     * readers never block on a concurrent writer; anything else means they can,
+     * which is the precondition for the "database is locked" failures in issue
+     * #238. Surfaced via `codegraph status` and the `codegraph_status` MCP tool.
+     */
+    getJournalMode(): string;
+    /**
+     * Get a node by ID
+     */
+    getNode(id: string): Node | null;
+    /**
+     * Get all nodes in a file
+     */
+    getNodesInFile(filePath: string): Node[];
+    /**
+     * Get all nodes of a specific kind
+     */
+    getNodesByKind(kind: Node['kind']): Node[];
+    /**
+     * Get ALL nodes with an exact name (direct index lookup, not FTS-ranked/capped).
+     * Used to enumerate every overload of a heavily-overloaded name so the specific
+     * definition the caller wants is never dropped below a search cut.
+     */
+    getNodesByName(name: string): Node[];
+    /**
+     * Search nodes by text
+     */
+    searchNodes(query: string, options?: SearchOptions): SearchResult[];
+    /**
+     * Find the project's "primary route file" — the file with the densest
+     * concentration of framework-emitted `route` nodes (≥3 routes, ≥30%
+     * of all non-test routes). Used to inline the routing config in
+     * `codegraph_explore` responses on small realworld template repos
+     * (rails-realworld, laravel-realworld, drupal-admintoolbar, …) where
+     * Glob+Read of `routes.rb`/`urls.py`/etc. otherwise beats codegraph.
+     */
+    getTopRouteFile(): {
+        filePath: string;
+        routeCount: number;
+        totalRoutes: number;
+    } | null;
+    /**
+     * Build a URL → handler routing manifest from the index. Each entry
+     * pairs a route node (URL + method) with its handler function/method
+     * via the `references` edge that framework resolvers emit. Returns
+     * null when fewer than 3 valid (non-test) routes exist.
+     */
+    getRoutingManifest(limit?: number): {
+        entries: Array<{
+            url: string;
+            handler: string;
+            handlerFile: string;
+            handlerLine: number;
+            handlerKind: string;
+        }>;
+        topHandlerFile: string | null;
+        topHandlerFileCount: number;
+        totalRoutes: number;
+    } | null;
+    /**
+     * Get outgoing edges from a node
+     */
+    getOutgoingEdges(nodeId: string): Edge[];
+    /**
+     * Get incoming edges to a node
+     */
+    getIncomingEdges(nodeId: string): Edge[];
+    /**
+     * Get a file record by path
+     */
+    getFile(filePath: string): FileRecord | null;
+    /**
+     * Get all tracked files
+     */
+    getFiles(): FileRecord[];
+    /**
+     * Get the context for a node (ancestors, children, references)
+     *
+     * Returns comprehensive context about a node including its containment
+     * hierarchy, children, incoming/outgoing references, type information,
+     * and relevant imports.
+     *
+     * @param nodeId - ID of the focal node
+     * @returns Context object with all related information
+     */
+    getContext(nodeId: string): Context;
+    /**
+     * Traverse the graph from a starting node
+     *
+     * Uses breadth-first search by default. Supports filtering by edge types,
+     * node types, and traversal direction.
+     *
+     * @param startId - Starting node ID
+     * @param options - Traversal options
+     * @returns Subgraph containing traversed nodes and edges
+     */
+    traverse(startId: string, options?: TraversalOptions): Subgraph;
+    /**
+     * Get the call graph for a function
+     *
+     * Returns both callers (functions that call this function) and
+     * callees (functions called by this function) up to the specified depth.
+     *
+     * @param nodeId - ID of the function/method node
+     * @param depth - Maximum depth in each direction (default: 2)
+     * @returns Subgraph containing the call graph
+     */
+    getCallGraph(nodeId: string, depth?: number): Subgraph;
+    /**
+     * Get the type hierarchy for a class/interface
+     *
+     * Returns both ancestors (types this extends/implements) and
+     * descendants (types that extend/implement this).
+     *
+     * @param nodeId - ID of the class/interface node
+     * @returns Subgraph containing the type hierarchy
+     */
+    getTypeHierarchy(nodeId: string): Subgraph;
+    /**
+     * Find all usages of a symbol
+     *
+     * Returns all nodes that reference the specified symbol through
+     * any edge type (calls, references, type_of, etc.).
+     *
+     * @param nodeId - ID of the symbol node
+     * @returns Array of nodes and edges that reference this symbol
+     */
+    findUsages(nodeId: string): Array<{
+        node: Node;
+        edge: Edge;
+    }>;
+    /**
+     * Get callers of a function/method
+     *
+     * @param nodeId - ID of the function/method node
+     * @param maxDepth - Maximum depth to traverse (default: 1)
+     * @returns Array of nodes that call this function
+     */
+    getCallers(nodeId: string, maxDepth?: number): Array<{
+        node: Node;
+        edge: Edge;
+    }>;
+    /**
+     * Get callees of a function/method
+     *
+     * @param nodeId - ID of the function/method node
+     * @param maxDepth - Maximum depth to traverse (default: 1)
+     * @returns Array of nodes called by this function
+     */
+    getCallees(nodeId: string, maxDepth?: number): Array<{
+        node: Node;
+        edge: Edge;
+    }>;
+    /**
+     * Calculate the impact radius of a node
+     *
+     * Returns all nodes that could be affected by changes to this node.
+     *
+     * @param nodeId - ID of the node
+     * @param maxDepth - Maximum depth to traverse (default: 3)
+     * @returns Subgraph containing potentially impacted nodes
+     */
+    getImpactRadius(nodeId: string, maxDepth?: number): Subgraph;
+    /**
+     * Find the shortest path between two nodes
+     *
+     * @param fromId - Starting node ID
+     * @param toId - Target node ID
+     * @param edgeKinds - Edge types to consider (all if empty)
+     * @returns Array of nodes and edges forming the path, or null if no path exists
+     */
+    findPath(fromId: string, toId: string, edgeKinds?: Edge['kind'][]): Array<{
+        node: Node;
+        edge: Edge | null;
+    }> | null;
+    /**
+     * Get ancestors of a node in the containment hierarchy
+     *
+     * @param nodeId - ID of the node
+     * @returns Array of ancestor nodes from immediate parent to root
+     */
+    getAncestors(nodeId: string): Node[];
+    /**
+     * Get immediate children of a node
+     *
+     * @param nodeId - ID of the node
+     * @returns Array of child nodes
+     */
+    getChildren(nodeId: string): Node[];
+    /**
+     * Get dependencies of a file
+     *
+     * @param filePath - Path to the file
+     * @returns Array of file paths this file depends on
+     */
+    getFileDependencies(filePath: string): string[];
+    /**
+     * Get dependents of a file
+     *
+     * @param filePath - Path to the file
+     * @returns Array of file paths that depend on this file
+     */
+    getFileDependents(filePath: string): string[];
+    /**
+     * Find circular dependencies in the codebase
+     *
+     * @returns Array of cycles, each cycle is an array of file paths
+     */
+    findCircularDependencies(): string[][];
+    /**
+     * Find dead code (unreferenced symbols)
+     *
+     * @param kinds - Node kinds to check (default: functions, methods, classes)
+     * @returns Array of unreferenced nodes
+     */
+    findDeadCode(kinds?: Node['kind'][]): Node[];
+    /**
+     * Get complexity metrics for a node
+     *
+     * @param nodeId - ID of the node
+     * @returns Object containing various complexity metrics
+     */
+    getNodeMetrics(nodeId: string): {
+        incomingEdgeCount: number;
+        outgoingEdgeCount: number;
+        callCount: number;
+        callerCount: number;
+        childCount: number;
+        depth: number;
+    };
+    /**
+     * Get the source code for a node
+     *
+     * Reads the file and extracts the code between startLine and endLine.
+     *
+     * @param nodeId - ID of the node
+     * @returns Code string or null if not found
+     */
+    getCode(nodeId: string): Promise<string | null>;
+    /**
+     * Find relevant subgraph for a query
+     *
+     * Combines semantic search with graph traversal to find the most
+     * relevant nodes and their relationships for a given query.
+     *
+     * @param query - Natural language query describing the task
+     * @param options - Search and traversal options
+     * @returns Subgraph of relevant nodes and edges
+     */
+    findRelevantContext(query: string, options?: FindRelevantContextOptions): Promise<Subgraph>;
+    /**
+     * Build context for a task
+     *
+     * Creates comprehensive context by:
+     * 1. Running FTS search to find entry points
+     * 2. Expanding the graph around entry points
+     * 3. Extracting code blocks for key nodes
+     * 4. Formatting output for Claude
+     *
+     * @param input - Task description (string or {title, description})
+     * @param options - Build options (maxNodes, includeCode, format, etc.)
+     * @returns TaskContext object or formatted string (markdown/JSON)
+     */
+    buildContext(input: TaskInput, options?: BuildContextOptions): Promise<TaskContext | string>;
+    /**
+     * Optimize the database (vacuum and analyze)
+     */
+    optimize(): void;
+    /**
+     * Clear all data from the graph
+     */
+    clear(): void;
+    /**
+     * Alias for close() for backwards compatibility.
+     * @deprecated Use close() instead
+     */
+    destroy(): void;
+    /**
+     * Completely remove CodeGraph from the project.
+     * This closes the database and deletes the .CodeGraph directory.
+     *
+     * WARNING: This permanently deletes all CodeGraph data for the project.
+     */
+    uninitialize(): void;
+}
+export default CodeGraph;
+//# sourceMappingURL=index.d.ts.map

package/dist/installer/config-writer.d.ts

@@ -0,0 +1,28 @@
+/**
+ * Backwards-compat shim — original Claude-only writer functions.
+ *
+ * The installer now uses the multi-target architecture in
+ * `./targets/`. This file is preserved so existing imports (the test
+ * suite, downstream tooling) keep working unchanged. Each function
+ * delegates to the Claude target. New code should import the target
+ * registry from `./targets/registry` directly.
+ *
+ * @deprecated Use `targets/registry.ts` and the `AgentTarget`
+ *   abstraction instead.
+ */
+export type InstallLocation = 'global' | 'local';
+/**
+ * Each shim calls ONLY the named per-file helper — writeMcpConfig
+ * writes only the MCP JSON, writePermissions only settings.json. The
+ * full multi-file install lives in `claudeTarget.install()` which the
+ * new orchestrator uses.
+ *
+ * There is no `writeClaudeMd` shim anymore: codegraph stopped writing a
+ * CLAUDE.md instructions block (issue #529) now that the MCP server's
+ * `initialize` instructions are the single source of truth.
+ */
+export declare function writeMcpConfig(location: InstallLocation): void;
+export declare function writePermissions(location: InstallLocation): void;
+export declare function hasMcpConfig(location: InstallLocation): boolean;
+export declare function hasPermissions(location: InstallLocation): boolean;
+//# sourceMappingURL=config-writer.d.ts.map

package/dist/installer/index.d.ts

@@ -0,0 +1,100 @@
+/**
+ * CodeGraph Interactive Installer
+ *
+ * Multi-target: writes MCP server config + instructions for the
+ * agents the user picks (Claude Code, Cursor, Codex CLI, opencode,
+ * Hermes Agent, Gemini CLI, Antigravity IDE).
+ * Defaults to the Claude-only behavior for backwards compatibility
+ * when no targets are explicitly chosen and nothing else is detected.
+ *
+ * Uses @clack/prompts for the interactive UI; `runInstallerWithOptions`
+ * is the non-interactive entry point used by the `--target` /
+ * `--print-config` CLI flags.
+ */
+import type { AgentTarget, Location, TargetId } from './targets/types';
+export { writeMcpConfig, writePermissions, hasMcpConfig, hasPermissions, } from './config-writer';
+export type { InstallLocation } from './config-writer';
+export interface RunInstallerOptions {
+    /** Comma-separated target list, or `auto` / `all` / `none`. */
+    target?: string;
+    /** Skip the location prompt; use this value directly. */
+    location?: Location;
+    /** Skip the auto-allow prompt; use this value directly. */
+    autoAllow?: boolean;
+    /**
+     * Skip every confirm and use defaults: location=global,
+     * autoAllow=true, target=auto. For scripting / CI.
+     */
+    yes?: boolean;
+}
+/**
+ * Interactive entry point — preserves the historical UX (`codegraph
+ * install` with no args goes through the prompts), but now starts
+ * the targets multi-select pre-populated with detected agents.
+ */
+export declare function runInstaller(): Promise<void>;
+export declare function runInstallerWithOptions(opts: RunInstallerOptions): Promise<void>;
+export interface RunUninstallerOptions {
+    /**
+     * Comma-separated target list, or `auto` / `all` / `none`. Defaults
+     * to `all` — uninstall sweeps every known agent and reports which
+     * ones it actually touched, so the user doesn't have to know where
+     * they configured it.
+     */
+    target?: string;
+    /** Skip the location prompt; use this value directly. */
+    location?: Location;
+    /** Non-interactive: location=global, target=all, no prompts. */
+    yes?: boolean;
+}
+export type UninstallStatus = 'removed' | 'not-configured' | 'unsupported';
+/**
+ * Per-target outcome of an uninstall sweep. `removed` means we deleted
+ * at least one thing; `not-configured` means the agent had no codegraph
+ * config at this location (nothing to do); `unsupported` means the
+ * agent has no config concept for this location (e.g. Codex is
+ * global-only, so a `local` uninstall skips it).
+ */
+export interface UninstallReport {
+    id: TargetId;
+    displayName: string;
+    status: UninstallStatus;
+    /** Absolute paths we actually edited/removed (action === 'removed'). */
+    removedPaths: string[];
+    /** Verbatim notes from the target (rare for uninstall). */
+    notes: string[];
+}
+/**
+ * Pure uninstall sweep — no prompts, no I/O beyond the targets' own
+ * file edits. Exposed (and unit-tested) separately from the clack UI in
+ * `runUninstaller` so the aggregation logic can be asserted directly.
+ *
+ * Each target's `uninstall()` is already safe to call when nothing was
+ * installed (it returns `not-found` actions), so this is safe to run
+ * across every target unconditionally.
+ */
+export declare function uninstallTargets(targets: readonly AgentTarget[], location: Location): UninstallReport[];
+/**
+ * Interactive uninstaller — the inverse of `runInstallerWithOptions`.
+ * Asks global-vs-local first (unless `--location`/`--yes` is given),
+ * then sweeps every agent target (or the `--target` subset) and prints
+ * one block per agent so the user sees exactly which providers it hit.
+ *
+ * Removes only what install wrote (MCP server entry, instructions
+ * block, permissions) — never the `.codegraph/` index, which `codegraph
+ * uninit` owns.
+ */
+export declare function runUninstaller(opts: RunUninstallerOptions): Promise<void>;
+/**
+ * When the live file watcher will be disabled for this project (e.g. WSL2
+ * /mnt drives, or CODEGRAPH_NO_WATCH), the index would silently go stale.
+ * Explain that, and offer to keep it fresh automatically via git hooks
+ * (commit / pull / checkout) instead of manual `codegraph sync`.
+ *
+ * No-op on environments where the watcher runs normally, so it's safe to
+ * call unconditionally after init.
+ */
+export declare function offerWatchFallback(clack: typeof import('@clack/prompts'), projectPath: string, opts?: {
+    yes?: boolean;
+}): Promise<void>;
+//# sourceMappingURL=index.d.ts.map

package/dist/installer/instructions-template.d.ts

@@ -0,0 +1,18 @@
+/**
+ * Marker constants for the legacy agent-instructions block.
+ *
+ * Codegraph used to write a `## CodeGraph` usage guide into each
+ * agent's instructions file (CLAUDE.md / AGENTS.md / GEMINI.md /
+ * codegraph.mdc / Kiro steering doc). That duplicated the guidance the
+ * MCP server already emits in its `initialize` response — every agent
+ * read the same playbook twice each turn (issue #529). The installer no
+ * longer writes an instructions file; the MCP server instructions in
+ * `mcp/server-instructions.ts` are the single source of truth.
+ *
+ * These markers are retained so install (self-heal on upgrade) and
+ * uninstall can find and strip the block a previous install wrote.
+ */
+/** Markers used by the marker-based section removal. */
+export declare const CODEGRAPH_SECTION_START = "<!-- CODEGRAPH_START -->";
+export declare const CODEGRAPH_SECTION_END = "<!-- CODEGRAPH_END -->";
+//# sourceMappingURL=instructions-template.d.ts.map