@colbymchenry/codegraph 1.1.0 → 1.1.1

package/README.md

@@ -747,6 +747,8 @@ Framework routing is validated the same way, on a canonical app per framework: E
 
 **MCP server not connecting** — Your agent starts the server itself, so you don't launch it by hand. Make sure the project is initialized and indexed (`codegraph status`) and that the path in your MCP config is correct. If it still won't connect, re-run `codegraph install` to rewrite the config.
 
+**MCP tool calls fail with `Transport closed` while `codegraph status`/`sync` are healthy** — almost always WSL2 with the project on a Windows drive (a `/mnt/c` or `/mnt/d` path), where the local socket CodeGraph uses to share one background server across sessions is unreliable. CodeGraph now falls back to serving the session in-process instead of dropping the connection, but if you still hit it, set `CODEGRAPH_NO_DAEMON=1` in your MCP server's environment to skip the shared server entirely (each session runs in its own process). Moving the project onto the Linux-native filesystem (e.g. under `~/` instead of `/mnt/`) restores the shared server.
+
 **Missing symbols** — The MCP server auto-syncs on save (wait a couple seconds). Run `codegraph sync` manually if needed. Check that the file's language is supported and isn't inside a `.gitignore`d or default-excluded directory (e.g. `node_modules`, `dist`).
 
 **Sharing one checkout between Windows and WSL** — Don't point both at the same `.codegraph/`: the background-server lock and the SQLite index are tied to the OS that wrote them, and SQLite locking across the WSL2/Windows filesystem boundary is unreliable. Give each side its own index in the same tree by setting `CODEGRAPH_DIR` to a distinct name on one of them — e.g. `CODEGRAPH_DIR=.codegraph-win` on Windows, leaving WSL on the default `.codegraph`. CodeGraph skips any sibling `.codegraph-*` directory when indexing and watching, so the two never trip over each other.

package/dist/extraction/index.d.ts

@@ -82,9 +82,12 @@ export declare class ScopeIgnore {
 export declare function buildScopeIgnore(rootDir: string, embeddedRoots?: Iterable<string>): ScopeIgnore;
 /**
  * Standalone discovery of every embedded repo root under `rootDir` (relative,
- * trailing-slashed) — both the untracked kind (#193) and the gitignored kind
- * (#514), recursively (an embedded repo can embed further repos). Returns []
- * for non-git roots: the filesystem walk handles nested repos there already.
+ * trailing-slashed) — the untracked kind (#193) always, and the gitignored kind
+ * (#514) only for directories the project opted in via `codegraph.json`
+ * `includeIgnored` (#622, #699); otherwise `.gitignore` is respected and they
+ * are not discovered (#970, #976). Recursive (an embedded repo can embed further
+ * repos). Returns [] for non-git roots: the filesystem walk handles nested repos
+ * there already.
  */
 export declare function discoverEmbeddedRepoRoots(rootDir: string): string[];
 /**

package/dist/project-config.d.ts

@@ -4,6 +4,14 @@ export declare const PROJECT_CONFIG_FILENAME = "codegraph.json";
 export interface ProjectConfig {
     /** Map of custom file extension (`.foo`) to a supported language id. */
     extensions?: Record<string, string>;
+    /**
+     * Gitignore-style patterns naming gitignored directories whose embedded git
+     * repositories should be indexed anyway — the explicit opt-in to override
+     * `.gitignore` for nested-repo discovery (#622, #699). Absent/empty (the
+     * default) means `.gitignore` is fully respected: gitignored embedded repos
+     * are never discovered or indexed (#970, #976).
+     */
+    includeIgnored?: string[];
 }
 /**
  * Load the validated extension overrides for a project, mtime-cached.
@@ -14,6 +22,15 @@ export interface ProjectConfig {
  * map when there is no `codegraph.json` (the zero-config default).
  */
 export declare function loadExtensionOverrides(rootDir: string): Record<string, Language>;
+/**
+ * Load the validated `includeIgnored` patterns for a project, mtime-cached.
+ *
+ * These name gitignored directories whose embedded git repositories should be
+ * indexed despite `.gitignore` (#622, #699). An empty result — the zero-config
+ * default — means `.gitignore` is fully respected: gitignored embedded repos
+ * are never discovered or indexed (#970, #976).
+ */
+export declare function loadIncludeIgnoredPatterns(rootDir: string): string[];
 /** Test/maintenance hook: forget cached config (e.g. after rewriting it in a test). */
 export declare function clearProjectConfigCache(): void;
 //# sourceMappingURL=project-config.d.ts.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@colbymchenry/codegraph",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "description": "Local-first code intelligence for AI agents (MCP). Self-contained — bundles its own runtime.",
   "bin": {
     "codegraph": "npm-shim.js"
@@ -15,12 +15,12 @@
     "./package.json": "./package.json"
   },
   "optionalDependencies": {
-    "@colbymchenry/codegraph-darwin-arm64": "1.1.0",
-    "@colbymchenry/codegraph-darwin-x64": "1.1.0",
-    "@colbymchenry/codegraph-linux-arm64": "1.1.0",
-    "@colbymchenry/codegraph-linux-x64": "1.1.0",
-    "@colbymchenry/codegraph-win32-arm64": "1.1.0",
-    "@colbymchenry/codegraph-win32-x64": "1.1.0"
+    "@colbymchenry/codegraph-darwin-arm64": "1.1.1",
+    "@colbymchenry/codegraph-darwin-x64": "1.1.1",
+    "@colbymchenry/codegraph-linux-arm64": "1.1.1",
+    "@colbymchenry/codegraph-linux-x64": "1.1.1",
+    "@colbymchenry/codegraph-win32-arm64": "1.1.1",
+    "@colbymchenry/codegraph-win32-x64": "1.1.1"
   },
   "files": [
     "npm-shim.js",