@danielblomma/cortex-mcp 2.0.9 → 2.0.13

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@danielblomma/cortex-mcp",
   "mcpName": "io.github.DanielBlomma/cortex",
-  "version": "2.0.9",
+  "version": "2.0.13",
   "description": "Local, repo-scoped context platform for coding assistants. Semantic search, graph relationships, and architectural rule context.",
   "type": "module",
   "author": "Daniel Blomma",

package/scaffold/mcp/package.json

@@ -9,7 +9,8 @@
     "graph:load": "npm run build --silent && node dist/loadGraph.js",
     "dev": "node --loader ts-node/esm src/server.ts",
     "start": "node dist/server.js",
-    "test": "npm run build --silent && node --test tests/*.test.mjs"
+    "test": "npm run build --silent && node --test tests/*.test.mjs",
+    "test:ci": "npm run build --silent && node --test --test-reporter=spec tests/*.test.mjs"
   },
   "dependencies": {
     "@huggingface/transformers": "^4.1.0",

package/scaffold/mcp/src/daemon/skill-sync-checker.ts

@@ -46,6 +46,7 @@ type ManifestEntry = {
 };
 
 type LocalSkillRecord = {
+  cli: SkillCli;
   scope: string;
   updated_at: string;
   path: string;
@@ -88,7 +89,29 @@ function readState(): LocalSkillsState {
   if (!existsSync(path)) return { skills: {} };
   try {
     const parsed = JSON.parse(readFileSync(path, "utf8")) as LocalSkillsState;
-    return { skills: parsed.skills ?? {}, last_synced_at: parsed.last_synced_at };
+    const normalizedSkills: Record<string, LocalSkillRecord> = {};
+    for (const [key, record] of Object.entries(parsed.skills ?? {})) {
+      if (!record || typeof record !== "object") continue;
+      const inferredCli =
+        record.path?.includes("/.codex/skills/")
+          ? "codex"
+          : "claude";
+      const cli =
+        record.cli === "codex" || record.cli === "claude"
+          ? record.cli
+          : inferredCli;
+      const normalizedKey = key.includes(":") ? key : `${cli}:${key}`;
+      normalizedSkills[normalizedKey] = {
+        cli,
+        scope: String(record.scope ?? "global"),
+        updated_at: String(record.updated_at ?? ""),
+        path: String(record.path ?? ""),
+      };
+    }
+    return {
+      skills: normalizedSkills,
+      last_synced_at: parsed.last_synced_at,
+    };
   } catch {
     return { skills: {} };
   }
@@ -103,19 +126,22 @@ function writeState(state: LocalSkillsState): void {
 }
 
 /**
- * Resolve the on-disk SKILL.md path for a skill. Global skills live under
- * ~/.claude/skills (Claude Code's user-scope skills directory); cli:codex
- * skills live under ~/.codex/skills. cli:claude scope is treated as
- * Claude-only and lands in ~/.claude/skills.
+ * Resolve the on-disk SKILL.md path for a skill install target. Global
+ * skills are installed once per CLI, so the destination root depends on the
+ * active sync target rather than just the stored scope.
  */
-function skillFilePath(scope: string, name: string): string {
+function skillFilePath(cli: SkillCli, name: string): string {
   const root =
-    scope === "cli:codex"
+    cli === "codex"
       ? join(homedir(), ".codex", "skills")
       : join(homedir(), ".claude", "skills");
   return join(root, name, "SKILL.md");
 }
 
+function stateSkillKey(cli: SkillCli, name: string): string {
+  return `${cli}:${name}`;
+}
+
 function shouldSyncForCli(scope: string, cli: SkillCli): boolean {
   if (scope === "global") return true;
   return scope === `cli:${cli}`;
@@ -222,7 +248,8 @@ export async function runSkillSyncForCli(
 
   // Detect adds + changes
   for (const entry of relevantManifest) {
-    const local = state.skills[entry.name];
+    const skillKey = stateSkillKey(cli, entry.name);
+    const local = state.skills[skillKey];
     const isNew = !local;
     const isChanged =
       Boolean(local) &&
@@ -243,7 +270,7 @@ export async function runSkillSyncForCli(
       };
     }
 
-    const path = skillFilePath(entry.scope, entry.name);
+    const path = skillFilePath(cli, entry.name);
     try {
       writeSkillFile(path, body);
     } catch (err) {
@@ -257,7 +284,8 @@ export async function runSkillSyncForCli(
       };
     }
 
-    state.skills[entry.name] = {
+    state.skills[skillKey] = {
+      cli,
       scope: entry.scope,
       updated_at: entry.updated_at,
       path,
@@ -269,7 +297,10 @@ export async function runSkillSyncForCli(
   // dropped (or disabled). We only consider state entries whose scope
   // matches this cli, so we don't accidentally remove the other CLI's
   // skills when running a per-cli tick.
-  for (const [name, record] of Object.entries(state.skills)) {
+  for (const [skillKey, record] of Object.entries(state.skills)) {
+    if (record.cli !== cli) continue;
+    const [, name] = skillKey.split(":", 2);
+    if (!name) continue;
     if (!shouldSyncForCli(record.scope, cli)) continue;
     if (remoteByName.has(name)) continue;
     try {
@@ -277,7 +308,7 @@ export async function runSkillSyncForCli(
     } catch {
       // best-effort; if unlink fails the next tick will retry
     }
-    delete state.skills[name];
+    delete state.skills[skillKey];
     removed.push(name);
   }
 

package/scaffold/mcp/src/embed.ts

@@ -1,20 +1,15 @@
 import crypto from "node:crypto";
 import fs from "node:fs";
 import path from "node:path";
-import { fileURLToPath } from "node:url";
 import { env, pipeline } from "@huggingface/transformers";
 import { readJsonl, asString, asNumber, asBoolean } from "./jsonl.js";
+import { CACHE_DIR, PATHS } from "./paths.js";
 import type { JsonObject, JsonValue } from "./types.js";
 
-const __filename = fileURLToPath(import.meta.url);
-const __dirname = path.dirname(__filename);
-const REPO_ROOT = path.resolve(__dirname, "../..");
-const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
-const CACHE_DIR = path.join(CONTEXT_DIR, "cache");
-const EMBEDDINGS_DIR = path.join(CONTEXT_DIR, "embeddings");
-const EMBEDDINGS_PATH = path.join(EMBEDDINGS_DIR, "entities.jsonl");
-const EMBEDDINGS_MANIFEST_PATH = path.join(EMBEDDINGS_DIR, "manifest.json");
-const MODEL_CACHE_DIR = path.join(EMBEDDINGS_DIR, "models");
+const EMBEDDINGS_PATH = PATHS.embeddingsEntities;
+const EMBEDDINGS_MANIFEST_PATH = PATHS.embeddingsManifest;
+const MODEL_CACHE_DIR = PATHS.embeddingsModelCache;
+const EMBEDDINGS_DIR = path.dirname(EMBEDDINGS_PATH);
 
 const DEFAULT_MODEL_ID = "Xenova/all-MiniLM-L6-v2";
 const DEFAULT_MAX_TEXT_CHARS = 7000;

package/scaffold/mcp/src/loadGraph.ts

@@ -1,16 +1,10 @@
 import fs from "node:fs";
 import path from "node:path";
-import { fileURLToPath } from "node:url";
 import ryugraph, { type Connection, type PreparedStatement, type QueryResult, type RyuValue } from "ryugraph";
 import { readJsonl, asString, asNumber, asBoolean } from "./jsonl.js";
+import { CACHE_DIR, CONTEXT_DIR, DB_PATH } from "./paths.js";
 import type { JsonObject } from "./types.js";
 
-const __filename = fileURLToPath(import.meta.url);
-const __dirname = path.dirname(__filename);
-const REPO_ROOT = path.resolve(__dirname, "../..");
-const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
-const CACHE_DIR = path.join(CONTEXT_DIR, "cache");
-const DB_PATH = path.join(CONTEXT_DIR, "db", "graph.ryu");
 const ONTOLOGY_PATH = path.join(CONTEXT_DIR, "ontology.cypher");
 const BATCH_SIZE = 50;
 

package/scaffold/mcp/src/paths.ts

@@ -21,9 +21,45 @@ function normalizeForWsl(rawPath: string): string {
 }
 
 const PROJECT_ROOT_OVERRIDE = process.env.CORTEX_PROJECT_ROOT?.trim();
-export const REPO_ROOT = PROJECT_ROOT_OVERRIDE
-  ? path.resolve(normalizeForWsl(PROJECT_ROOT_OVERRIDE))
-  : path.resolve(__dirname, "../..");
+
+function hasContextConfig(candidate: string): boolean {
+  return fs.existsSync(path.join(candidate, ".context", "config.yaml"));
+}
+
+function resolveFrom(startDir: string): string | null {
+  let current = path.resolve(startDir);
+  while (true) {
+    if (hasContextConfig(current)) {
+      return current;
+    }
+
+    const parent = path.dirname(current);
+    if (parent === current) {
+      return null;
+    }
+    current = parent;
+  }
+}
+
+function resolveRepoRoot(): string {
+  const candidates = [
+    PROJECT_ROOT_OVERRIDE ? path.resolve(normalizeForWsl(PROJECT_ROOT_OVERRIDE)) : null,
+    process.cwd(),
+    __dirname,
+    process.env.INIT_CWD?.trim() ? path.resolve(normalizeForWsl(process.env.INIT_CWD.trim())) : null
+  ].filter((value): value is string => Boolean(value));
+
+  for (const candidate of candidates) {
+    const resolved = resolveFrom(candidate);
+    if (resolved) {
+      return resolved;
+    }
+  }
+
+  return path.resolve(__dirname, "../../..");
+}
+
+export const REPO_ROOT = resolveRepoRoot();
 export const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 export const CACHE_DIR = path.join(CONTEXT_DIR, "cache");
 export const DB_PATH = path.join(CONTEXT_DIR, "db", "graph.ryu");

package/scaffold/mcp/tests/paths.test.mjs

@@ -0,0 +1,38 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+import { mkdtempSync, mkdirSync, realpathSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import { spawnSync } from "node:child_process";
+import { pathToFileURL } from "node:url";
+
+test("paths resolve the project root from cwd without duplicating .context", () => {
+  const projectRoot = mkdtempSync(path.join(tmpdir(), "cortex-paths-"));
+  const contextDir = path.join(projectRoot, ".context");
+  const mcpDir = path.join(contextDir, "mcp");
+  const pathsModuleUrl = pathToFileURL(path.resolve("dist/paths.js")).href;
+
+  mkdirSync(mcpDir, { recursive: true });
+  writeFileSync(path.join(contextDir, "config.yaml"), "source_paths:\n  - src\n");
+
+  const result = spawnSync(
+    process.execPath,
+    [
+      "--input-type=module",
+      "-e",
+      `import { REPO_ROOT, CONTEXT_DIR, CACHE_DIR } from ${JSON.stringify(pathsModuleUrl)}; console.log(JSON.stringify({ REPO_ROOT, CONTEXT_DIR, CACHE_DIR }));`
+    ],
+    {
+      cwd: mcpDir,
+      encoding: "utf8"
+    }
+  );
+
+  assert.equal(result.status, 0, result.stderr);
+
+  const parsed = JSON.parse(result.stdout.trim());
+  const resolvedProjectRoot = realpathSync(projectRoot);
+  assert.equal(parsed.REPO_ROOT, resolvedProjectRoot);
+  assert.equal(parsed.CONTEXT_DIR, path.join(resolvedProjectRoot, ".context"));
+  assert.equal(parsed.CACHE_DIR, path.join(resolvedProjectRoot, ".context", "cache"));
+});

package/scaffold/scripts/embed.sh

@@ -12,4 +12,4 @@ fi
 mkdir -p "$MCP_DIR/.npm-cache"
 
 echo "[embed] generating embeddings via .context/mcp/embed"
-NPM_CONFIG_CACHE="$MCP_DIR/.npm-cache" npm --prefix "$MCP_DIR" run embed --silent -- "$@"
+CORTEX_PROJECT_ROOT="$REPO_ROOT" NPM_CONFIG_CACHE="$MCP_DIR/.npm-cache" npm --prefix "$MCP_DIR" run embed --silent -- "$@"

package/scaffold/scripts/load-ryu.sh

@@ -15,4 +15,4 @@ if [[ ! -d "$MCP_DIR/node_modules" ]]; then
   exit 1
 fi
 
-NPM_CONFIG_CACHE="$MCP_DIR/.npm-cache" npm --prefix "$MCP_DIR" run graph:load -- "$@"
+CORTEX_PROJECT_ROOT="$REPO_ROOT" NPM_CONFIG_CACHE="$MCP_DIR/.npm-cache" npm --prefix "$MCP_DIR" run graph:load -- "$@"