README: Kuzu lock note and LSP resolution wording

- Add note: close Cursor / disable MCP before full CLI reindex to avoid lock
- Clarify LSP order: workspace/repo first, then package node_modules
- chore: release v0.4.1

Made-with: Cursor

Author: chouswei

README.md

@@ -69,10 +69,12 @@ npx sysmledgraph clean
 **Options and environment:**
 
 - **`--storage <path>`** — Override the storage root (default: `~/.sysmledgraph`). Same as env **`SYSMEDGRAPH_STORAGE_ROOT`**.
-- **`SYSMLLSP_SERVER_PATH`** — Optional. Path to the sysml-v2-lsp server JS (e.g. `dist/server/server.js`). If unset, the CLI looks in local `node_modules` and then walks up from the current working directory (e.g. repo root when run from a subfolder like `tools/sysmledgraph`).
+- **`SYSMLLSP_SERVER_PATH`** — Optional. Path to the sysml-v2-lsp server JS (e.g. `dist/server/server.js`). If unset, the CLI looks in the current workspace/repo first (walk up from cwd), then in sysmledgraph’s `node_modules`.
 
 **Storage layout:** Under the storage root: `registry.json` (list of indexed paths), and `db/<sanitized-path>.kuzu` (one Kuzu database per indexed path). On failure, the CLI writes errors to stderr and exits non-zero.
 
+**Kuzu lock:** Only one process should open the same DB at a time. For a full CLI reindex, close Cursor (or disable the sysmledgraph MCP) first to avoid “Could not set lock on file”. See [docs/MCP-AND-KUZU.md](docs/MCP-AND-KUZU.md).
+
 ---
 
 ### MCP

package.json

@@ -1,6 +1,6 @@
 {
   "name": "sysmledgraph",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "description": "Path-only SysML indexer: knowledge graph (Kuzu), MCP server (query, context, impact, rename, cypher), CLI (analyze, list, clean)",
   "type": "module",
   "main": "dist/src/index.js",

release-notes-v0.4.1.md

@@ -0,0 +1,4 @@
+## Changes
+
+- **README: Kuzu lock note** — Added a short note in the CLI section: for a full CLI reindex, close Cursor (or disable the sysmledgraph MCP) first to avoid "Could not set lock on file"; link to docs/MCP-AND-KUZU.md.
+- **README: LSP resolution** — Clarified that the CLI looks in the current workspace/repo first (walk up from cwd), then sysmledgraph's `node_modules`.