Add overlapping-paths bug fix tests and --global flag for refdocs add

Cover the isPathCovered overlapping-paths fix with unit and integration
tests, add findMarkdownFiles dedup tests, and implement a --global flag
across all CLI commands to store/search docs at ~/.refdocs/ with
automatic local+global result merging.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: Chris Arter

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@dynamik-dev/refdocs",
-  "version": "0.3.0",
+  "version": "0.4.0",
   "type": "module",
   "description": "Local CLI tool that indexes markdown documentation and exposes fast fuzzy search with intelligent chunking",
   "main": "dist/src/index.js",

src/add.ts

@@ -34,7 +34,10 @@ export async function addFromUrl(
   const parsed = parseGitHubUrl(url);
   const branch = options.branch ?? parsed.branch ?? undefined;
   const token = options.token ?? process.env.GITHUB_TOKEN ?? undefined;
-  const localPath = options.path ?? `ref-docs/${parsed.repo}`;
+  const defaultPath = parsed.subpath
+    ? `ref-docs/${parsed.owner}/${parsed.repo}/${parsed.subpath}`
+    : `ref-docs/${parsed.owner}/${parsed.repo}`;
+  const localPath = options.path ?? defaultPath;
 
   const tarball = await downloadTarball(parsed.owner, parsed.repo, branch, token);
 
@@ -54,7 +57,7 @@ export async function addFromUrl(
     addedAt: new Date().toISOString(),
   };
 
-  const paths = config.paths.includes(localPath)
+  const paths = isPathCovered(config.paths, localPath)
     ? config.paths
     : [...config.paths, localPath];
 
@@ -217,6 +220,12 @@ function stripTarPrefix(entryName: string): string {
   return parts.slice(1).join("/");
 }
 
+export function isPathCovered(existingPaths: string[], newPath: string): boolean {
+  return existingPaths.some(
+    (p) => p === newPath || newPath.startsWith(p + "/"),
+  );
+}
+
 function upsertSource(sources: Source[], newSource: Source): Source[] {
   const key = `${newSource.owner}/${newSource.repo}/${newSource.subpath}`;
   const filtered = sources.filter(

src/config.ts

@@ -1,5 +1,6 @@
-import { readFileSync, writeFileSync, existsSync } from "node:fs";
+import { readFileSync, writeFileSync, existsSync, mkdirSync } from "node:fs";
 import { join, dirname, resolve } from "node:path";
+import { homedir } from "node:os";
 import type { RefdocsConfig, Source } from "./types.js";
 
 export const CONFIG_FILENAME = ".refdocs.json";
@@ -128,3 +129,42 @@ export function saveConfig(config: Partial<RefdocsConfig>, configDir: string): v
   const merged = { ...existing, ...config };
   writeFileSync(configPath, JSON.stringify(merged, null, 2) + "\n", "utf-8");
 }
+
+let globalDirOverride: string | null = null;
+
+export function setGlobalDirOverride(dir: string | null): void {
+  globalDirOverride = dir;
+}
+
+export function getGlobalConfigDir(): string {
+  return globalDirOverride ?? join(homedir(), ".refdocs");
+}
+
+export function initGlobalConfig(): void {
+  const globalDir = getGlobalConfigDir();
+  mkdirSync(globalDir, { recursive: true });
+  const configPath = join(globalDir, CONFIG_FILENAME);
+  if (existsSync(configPath)) return;
+  const globalDefault: RefdocsConfig = {
+    ...DEFAULT_CONFIG,
+    paths: ["docs"],
+  };
+  writeFileSync(configPath, JSON.stringify(globalDefault, null, 2) + "\n", "utf-8");
+}
+
+export function loadGlobalConfig(): ConfigResult | null {
+  const globalDir = getGlobalConfigDir();
+  const configPath = join(globalDir, CONFIG_FILENAME);
+  if (!existsSync(configPath)) return null;
+  try {
+    const raw = JSON.parse(readFileSync(configPath, "utf-8"));
+    const errors = validateConfig(raw);
+    if (errors.length > 0) return null;
+    return {
+      config: { ...DEFAULT_CONFIG, ...raw, boostFields: { ...DEFAULT_CONFIG.boostFields, ...raw.boostFields } },
+      configDir: globalDir,
+    };
+  } catch {
+    return null;
+  }
+}