@optave/codegraph 3.12.0 → 3.15.0

package/src/infrastructure/registry.ts

@@ -1,6 +1,7 @@
 import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
+import type { ConsentDecision } from '../types.js';
 import { debug, warn } from './logger.js';
 
 export const REGISTRY_PATH: string =
@@ -16,8 +17,15 @@ interface RegistryEntry {
   lastAccessedAt?: string;
 }
 
+interface UserConfigSection {
+  /** Per-repo consent decisions keyed by absolute repo path. */
+  consent: Record<string, ConsentDecision>;
+}
+
 interface Registry {
   repos: Record<string, RegistryEntry>;
+  /** User-level global config consent store — separate from MCP repo listings. */
+  userConfig?: UserConfigSection;
 }
 
 /**
@@ -160,6 +168,67 @@ export function resolveRepoDbPath(
   return entry.dbPath;
 }
 
+// ── User-config consent ────────────────────────────────────────────────
+
+/**
+ * Read the per-repo consent decision for the global user config.
+ * Returns `undefined` when the repo is undecided (no recorded decision).
+ */
+export function getUserConfigConsent(
+  rootDir: string,
+  registryPath: string = REGISTRY_PATH,
+): ConsentDecision | undefined {
+  const registry = loadRegistry(registryPath);
+  const absRoot = path.resolve(rootDir);
+  return registry.userConfig?.consent?.[absRoot];
+}
+
+/**
+ * Persist a per-repo consent decision. Atomic write via temp+rename.
+ */
+export function setUserConfigConsent(
+  rootDir: string,
+  decision: ConsentDecision,
+  registryPath: string = REGISTRY_PATH,
+): void {
+  const registry = loadRegistry(registryPath);
+  const absRoot = path.resolve(rootDir);
+  if (!registry.userConfig) registry.userConfig = { consent: {} };
+  if (!registry.userConfig.consent) registry.userConfig.consent = {};
+  registry.userConfig.consent[absRoot] = decision;
+  saveRegistry(registry, registryPath);
+  debug(`User-config consent for "${absRoot}" set to "${decision}"`);
+}
+
+/**
+ * List every repo with a recorded consent decision, sorted by path.
+ */
+export function listUserConfigConsent(
+  registryPath: string = REGISTRY_PATH,
+): Array<{ path: string; decision: ConsentDecision }> {
+  const registry = loadRegistry(registryPath);
+  const consent = registry.userConfig?.consent ?? {};
+  return Object.entries(consent)
+    .map(([p, decision]) => ({ path: p, decision }))
+    .sort((a, b) => a.path.localeCompare(b.path));
+}
+
+/**
+ * Revert a repo to undecided state. Returns true if a decision was removed.
+ */
+export function clearUserConfigConsent(
+  rootDir: string,
+  registryPath: string = REGISTRY_PATH,
+): boolean {
+  const registry = loadRegistry(registryPath);
+  const absRoot = path.resolve(rootDir);
+  const consent = registry.userConfig?.consent;
+  if (!consent || !(absRoot in consent)) return false;
+  delete consent[absRoot];
+  saveRegistry(registry, registryPath);
+  return true;
+}
+
 interface PrunedEntry {
   name: string;
   path: string;
@@ -173,19 +242,18 @@ interface PrunedEntry {
  *
  * When `dryRun` is true, entries are identified but not removed from disk.
  */
-export function pruneRegistry(
-  registryPath: string = REGISTRY_PATH,
-  ttlDays: number = DEFAULT_TTL_DAYS,
-  excludeNames: string[] = [],
-  dryRun = false,
+/**
+ * Walk `registry.repos`, identify entries that are missing on disk or have
+ * exceeded the TTL, and optionally delete them (when `dryRun` is false).
+ * Returns the list of entries that were (or would be) pruned.
+ */
+function pruneRepoEntries(
+  registry: Registry,
+  cutoff: number,
+  excludeSet: Set<string>,
+  dryRun: boolean,
 ): PrunedEntry[] {
-  const registry = loadRegistry(registryPath);
   const pruned: PrunedEntry[] = [];
-  const cutoff = Date.now() - ttlDays * 24 * 60 * 60 * 1000;
-  const excludeSet = new Set(
-    excludeNames.filter((n) => typeof n === 'string' && n.trim().length > 0),
-  );
-
   for (const [name, entry] of Object.entries(registry.repos)) {
     if (excludeSet.has(name)) continue;
     if (!fs.existsSync(entry.path)) {
@@ -199,8 +267,45 @@ export function pruneRegistry(
       if (!dryRun) delete registry.repos[name];
     }
   }
+  return pruned;
+}
+
+/**
+ * Prune consent entries whose repo paths no longer exist on disk.
+ * Consent entries are TTL-exempt — only the missing-path rule applies.
+ * Returns true when at least one entry was removed.
+ */
+function pruneConsentEntries(consent: Record<string, ConsentDecision>): boolean {
+  let changed = false;
+  for (const p of Object.keys(consent)) {
+    if (!fs.existsSync(p)) {
+      delete consent[p];
+      changed = true;
+    }
+  }
+  return changed;
+}
+
+export function pruneRegistry(
+  registryPath: string = REGISTRY_PATH,
+  ttlDays: number = DEFAULT_TTL_DAYS,
+  excludeNames: string[] = [],
+  dryRun = false,
+): PrunedEntry[] {
+  const registry = loadRegistry(registryPath);
+  const cutoff = Date.now() - ttlDays * 24 * 60 * 60 * 1000;
+  const excludeSet = new Set(
+    excludeNames.filter((n) => typeof n === 'string' && n.trim().length > 0),
+  );
+
+  const pruned = pruneRepoEntries(registry, cutoff, excludeSet, dryRun);
+
+  const consentChanged =
+    !dryRun && registry.userConfig?.consent
+      ? pruneConsentEntries(registry.userConfig.consent)
+      : false;
 
-  if (!dryRun && pruned.length > 0) {
+  if (!dryRun && (pruned.length > 0 || consentChanged)) {
     saveRegistry(registry, registryPath);
   }
 

package/src/infrastructure/update-check.ts

@@ -61,6 +61,33 @@ function saveCache(cache: UpdateCache, cachePath: string = CACHE_PATH): void {
   fs.renameSync(tmp, cachePath);
 }
 
+/**
+ * Collect the full response body from an IncomingMessage stream.
+ * Resolves with the body string, or null on parse/status error.
+ */
+function collectResponseBody(res: import('node:http').IncomingMessage): Promise<string | null> {
+  return new Promise((resolve) => {
+    if (res.statusCode !== 200) {
+      res.resume();
+      resolve(null);
+      return;
+    }
+    let body = '';
+    res.setEncoding('utf-8');
+    res.on('data', (chunk: string) => {
+      body += chunk;
+    });
+    res.on('end', () => {
+      try {
+        const data = JSON.parse(body);
+        resolve(typeof data.version === 'string' ? data.version : null);
+      } catch {
+        resolve(null);
+      }
+    });
+  });
+}
+
 /**
  * Fetch the latest version string from the npm registry.
  * Returns the version string or null on failure.
@@ -71,24 +98,7 @@ function fetchLatestVersion(): Promise<string | null> {
       REGISTRY_URL,
       { timeout: FETCH_TIMEOUT_MS, headers: { Accept: 'application/json' } },
       (res) => {
-        if (res.statusCode !== 200) {
-          res.resume();
-          resolve(null);
-          return;
-        }
-        let body = '';
-        res.setEncoding('utf-8');
-        res.on('data', (chunk: string) => {
-          body += chunk;
-        });
-        res.on('end', () => {
-          try {
-            const data = JSON.parse(body);
-            resolve(typeof data.version === 'string' ? data.version : null);
-          } catch {
-            resolve(null);
-          }
-        });
+        collectResponseBody(res).then(resolve);
       },
     );
     req.on('error', () => resolve(null));
@@ -109,6 +119,32 @@ interface CheckForUpdatesOptions {
   _fetchLatest?: () => Promise<string | null>;
 }
 
+/**
+ * Return the latest version from cache if fresh, or fetch it from the registry.
+ * Persists the fetched version to the cache only when a network fetch occurs
+ * (i.e. the cache is stale or missing). Returns the cached value directly
+ * without updating the cache when the cache is still within `CACHE_TTL_MS`.
+ * Returns null when the network fetch fails or the cache is corrupt.
+ */
+async function resolveLatestVersion(
+  cachePath: string,
+  fetchFn: () => Promise<string | null>,
+): Promise<string | null> {
+  const cache = loadCache(cachePath);
+
+  if (cache && Date.now() - cache.lastCheckedAt < CACHE_TTL_MS) {
+    // Cache is fresh — use stored value directly
+    return cache.latestVersion;
+  }
+
+  // Cache is stale or missing — fetch from registry
+  const latest = await fetchFn();
+  if (!latest) return null;
+
+  saveCache({ lastCheckedAt: Date.now(), latestVersion: latest }, cachePath);
+  return latest;
+}
+
 /**
  * Check whether a newer version of codegraph is available.
  *
@@ -129,23 +165,9 @@ export async function checkForUpdates(
   const fetchFn = options._fetchLatest || fetchLatestVersion;
 
   try {
-    const cache = loadCache(cachePath);
-
-    // Cache is fresh — use it
-    if (cache && Date.now() - cache.lastCheckedAt < CACHE_TTL_MS) {
-      if (semverCompare(currentVersion, cache.latestVersion) < 0) {
-        return { current: currentVersion, latest: cache.latestVersion };
-      }
-      return null;
-    }
-
-    // Cache is stale or missing — fetch
-    const latest = await fetchFn();
+    const latest = await resolveLatestVersion(cachePath, fetchFn);
     if (!latest) return null;
 
-    // Update cache regardless of result
-    saveCache({ lastCheckedAt: Date.now(), latestVersion: latest }, cachePath);
-
     if (semverCompare(currentVersion, latest) < 0) {
       return { current: currentVersion, latest };
     }

package/src/mcp/server.ts

@@ -20,6 +20,7 @@ import type { CodegraphConfig, MCPServerOptions } from '../types.js';
 import { initMcpDefaults } from './middleware.js';
 import { buildToolList } from './tool-registry.js';
 import { TOOL_HANDLERS } from './tools/index.js';
+import type { McpToolContext } from './types.js';
 
 /**
  * Module-level guard to register shutdown handlers only once per process.
@@ -28,14 +29,7 @@ import { TOOL_HANDLERS } from './tools/index.js';
  */
 let _activeServer: any = null;
 
-export interface McpToolContext {
-  dbPath: string | undefined;
-  getQueries(): Promise<any>;
-  getDatabase(): any;
-  findDbPath: typeof findDbPath;
-  allowedRepos: string[] | undefined;
-  MCP_MAX_LIMIT: number;
-}
+export type { McpToolContext };
 
 interface MCPServerOptionsInternal extends MCPServerOptions {
   config?: CodegraphConfig;

package/src/mcp/tools/ast-query.ts

@@ -1,6 +1,6 @@
 import type { ASTNodeKind } from '../../types.js';
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'ast_query';
 

package/src/mcp/tools/audit.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'audit';
 

package/src/mcp/tools/batch-query.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'batch_query';
 

package/src/mcp/tools/branch-compare.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'branch_compare';
 

package/src/mcp/tools/brief.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'brief';
 

package/src/mcp/tools/cfg.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'cfg';
 

package/src/mcp/tools/check.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'check';
 

package/src/mcp/tools/co-changes.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'co_changes';
 

package/src/mcp/tools/code-owners.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'code_owners';
 

package/src/mcp/tools/communities.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'communities';
 

package/src/mcp/tools/complexity.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'complexity';
 

package/src/mcp/tools/context.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'context';
 

package/src/mcp/tools/dataflow.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'dataflow';
 

package/src/mcp/tools/diff-impact.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'diff_impact';
 

package/src/mcp/tools/execution-flow.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'execution_flow';
 

package/src/mcp/tools/export-graph.ts

@@ -1,6 +1,6 @@
 import { findDbPath } from '../../db/index.js';
 import { effectiveOffset, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'export_graph';
 

package/src/mcp/tools/file-deps.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'file_deps';
 

package/src/mcp/tools/file-exports.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'file_exports';
 

package/src/mcp/tools/find-cycles.ts

@@ -1,6 +1,6 @@
 import { findDbPath } from '../../db/index.js';
 import { findCycles } from '../../domain/graph/cycles.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'find_cycles';
 

package/src/mcp/tools/fn-impact.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'fn_impact';
 

package/src/mcp/tools/impact-analysis.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'impact_analysis';
 

package/src/mcp/tools/implementations.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'implementations';
 

package/src/mcp/tools/index.ts

@@ -2,12 +2,9 @@
  * Barrel module — registers all MCP tool handlers.
  */
 
-import type { McpToolContext } from '../server.js';
+import type { McpToolHandler } from '../types.js';
 
-export interface McpToolHandler {
-  name: string;
-  handler(args: any, ctx: McpToolContext): Promise<unknown>;
-}
+export type { McpToolContext, McpToolHandler } from '../types.js';
 
 import * as astQuery from './ast-query.js';
 import * as audit from './audit.js';

package/src/mcp/tools/interfaces.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'interfaces';
 

package/src/mcp/tools/list-functions.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'list_functions';
 

package/src/mcp/tools/list-repos.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'list_repos';
 

package/src/mcp/tools/module-map.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'module_map';
 

package/src/mcp/tools/node-roles.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'node_roles';
 

package/src/mcp/tools/path.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'path';
 

package/src/mcp/tools/query.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'query';
 

package/src/mcp/tools/semantic-search.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'semantic_search';
 

package/src/mcp/tools/sequence.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'sequence';
 

package/src/mcp/tools/structure.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'structure';
 

package/src/mcp/tools/symbol-children.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'symbol_children';
 

package/src/mcp/tools/triage.ts

@@ -1,6 +1,6 @@
 import type { Role } from '../../types.js';
 import { effectiveLimit, effectiveOffset, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'triage';
 

package/src/mcp/tools/where.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'where';
 

package/src/mcp/types.ts

@@ -0,0 +1,21 @@
+/**
+ * Shared MCP types used by server.ts and all tool modules.
+ * Extracted here to break the circular dependency between server.ts and tools/index.ts.
+ */
+
+import type Database from 'better-sqlite3';
+import type { findDbPath } from '../db/index.js';
+
+export interface McpToolContext {
+  dbPath: string | undefined;
+  getQueries(): Promise<any>;
+  getDatabase(): typeof Database;
+  findDbPath: typeof findDbPath;
+  allowedRepos: string[] | undefined;
+  MCP_MAX_LIMIT: number;
+}
+
+export interface McpToolHandler {
+  name: string;
+  handler(args: any, ctx: McpToolContext): Promise<unknown>;
+}

package/src/presentation/queries-cli/index.ts

@@ -9,5 +9,5 @@ export {
   queryName,
   where,
 } from './inspect.js';
-export { moduleMap, roles, stats } from './overview.js';
+export { dynamicCalls, moduleMap, roles, stats } from './overview.js';
 export { symbolPath } from './path.js';