fix(mcp): drop root .mcp.json so plugin's mcp-search isn't duplicated (#2411)

The repo shipped both a root-level .mcp.json and plugin/.mcp.json with
identical mcp-search launchers — kept in sync by a build-time guard and
a test. The root file was a holdover from when devs working inside the
repo could load mem-search without installing the plugin. With the
plugin universally installed, every plugin user now sees `/doctor` warn:

    Plugin (claude-mem @ plugin:claude-mem:mcp-search): MCP server
    "mcp-search" skipped — same command/URL as already-configured
    "mcp-search"

…because Claude Code dedupes by command and skips the plugin's
namespaced registration. The duplicate is functionally harmless but
suppresses the canonical `plugin:claude-mem:mcp-search` entry.

This removes the root .mcp.json entirely and re-points everything that
referenced it at the bundled plugin copy:

- .mcp.json: deleted
- .codex-plugin/plugin.json: mcpServers → ./plugin/.mcp.json
- package.json: drop .mcp.json from files
- scripts/build-hooks.js: drop root-file requirement + sync check
- scripts/sync-marketplace.cjs: drop syncManagedFiles entry
- src/npx-cli/commands/install.ts: drop from allowedTopLevelEntries
- tests/infrastructure/plugin-distribution.test.ts: drop two tests
  enforcing the now-removed root file

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

.codex-plugin/plugin.json

@@ -23,7 +23,7 @@
     "nodejs"
   ],
   "skills": "./plugin/skills/",
-  "mcpServers": "./.mcp.json",
+  "mcpServers": "./plugin/.mcp.json",
   "hooks": "./plugin/hooks/codex-hooks.json",
   "interface": {
     "displayName": "claude-mem",

.mcp.json

@@ -1,12 +0,0 @@
-{
-  "mcpServers": {
-    "mcp-search": {
-      "type": "stdio",
-      "command": "sh",
-      "args": [
-        "-c",
-        "_C=\"${CLAUDE_CONFIG_DIR:-$HOME/.claude}\"; _E=\"${CLAUDE_PLUGIN_ROOT:-${PLUGIN_ROOT:-}}\"; _P=$({ [ -n \"$_E\" ] && printf '%s\\n' \"$_E\"; printf '%s\\n' \"$PWD/plugin\" \"$PWD\"; ls -dt \"$HOME/.codex/plugins/cache/claude-mem-local/claude-mem\"/[0-9]*/ \"$HOME/.codex/plugins/cache/thedotmack/claude-mem\"/[0-9]*/ \"$_C/plugins/cache/thedotmack/claude-mem\"/[0-9]*/ 2>/dev/null; printf '%s\\n' \"$_C/plugins/marketplaces/thedotmack/plugin\"; } | while IFS= read -r _R; do [ -d \"$_R/plugin/scripts\" ] && _Q=\"$_R/plugin\" || _Q=\"$_R\"; [ -f \"$_Q/scripts/mcp-server.cjs\" ] && { printf '%s\\n' \"$_Q\"; break; }; done); [ -n \"$_P\" ] || { echo \"claude-mem: mcp server not found\" >&2; exit 1; }; exec node \"$_P/scripts/mcp-server.cjs\""
-      ]
-    }
-  }
-}

package.json

@@ -44,7 +44,6 @@
     "dist",
     ".agents/plugins/marketplace.json",
     ".codex-plugin",
-    ".mcp.json",
     "plugin/.claude-plugin",
     "plugin/.codex-plugin",
     "plugin/.mcp.json",

scripts/build-hooks.js

@@ -414,7 +414,6 @@ async function buildHooks() {
       'plugin/.codex-plugin/plugin.json',
       'plugin/.mcp.json',
       '.codex-plugin/plugin.json',
-      '.mcp.json',
       '.agents/plugins/marketplace.json',
     ];
     for (const filePath of requiredDistributionFiles) {
@@ -433,11 +432,7 @@ async function buildHooks() {
     if (claudeMemMarketplaceEntry?.source?.path !== './plugin') {
       throw new Error('.agents/plugins/marketplace.json must point claude-mem source.path at ./plugin so Codex loads the bundled plugin root');
     }
-    const rootMcp = JSON.parse(fs.readFileSync('.mcp.json', 'utf-8'));
     const bundledMcp = JSON.parse(fs.readFileSync('plugin/.mcp.json', 'utf-8'));
-    if (JSON.stringify(rootMcp.mcpServers?.['mcp-search']) !== JSON.stringify(bundledMcp.mcpServers?.['mcp-search'])) {
-      throw new Error('.mcp.json and plugin/.mcp.json mcp-search launchers must stay in sync');
-    }
     const mcpSearchCommand = bundledMcp.mcpServers?.['mcp-search']?.args?.join(' ') ?? '';
     if (!mcpSearchCommand.includes('.codex/plugins/cache/claude-mem-local/claude-mem')) {
       throw new Error('plugin/.mcp.json mcp-search launcher must include Codex cache fallback for hosts that do not inject PLUGIN_ROOT');

scripts/sync-marketplace.cjs

@@ -34,9 +34,7 @@ function getGitignoreExcludes(basePath) {
   const gitignorePath = path.join(basePath, '.gitignore');
   if (!existsSync(gitignorePath)) return '';
 
-  const syncManagedFiles = new Set([
-    '.mcp.json',
-  ]);
+  const syncManagedFiles = new Set();
 
   const lines = readFileSync(gitignorePath, 'utf-8').split('\n');
   return lines

src/npx-cli/commands/install.ts

@@ -527,7 +527,6 @@ function copyPluginToMarketplace(): void {
   const allowedTopLevelEntries = [
     '.agents',
     '.codex-plugin',
-    '.mcp.json',
     'plugin',
     'package.json',
     'package-lock.json',

tests/infrastructure/plugin-distribution.test.ts

@@ -90,13 +90,6 @@ describe('Plugin Distribution - Codex Marketplace', () => {
     expect(command).toContain('plugins/cache/thedotmack/claude-mem');
     expect(command).toContain('claude-mem: mcp server not found');
   });
-
-  it('keeps root and bundled MCP launchers in sync', () => {
-    const rootMcp = JSON.parse(readFileSync(path.join(projectRoot, '.mcp.json'), 'utf-8'));
-    const bundledMcp = JSON.parse(readFileSync(path.join(projectRoot, 'plugin/.mcp.json'), 'utf-8'));
-
-    expect(rootMcp.mcpServers['mcp-search']).toEqual(bundledMcp.mcpServers['mcp-search']);
-  });
 });
 
 describe('Plugin Distribution - hooks.json Integrity', () => {
@@ -134,7 +127,7 @@ describe('Plugin Distribution - hooks.json Integrity', () => {
 
 describe('Plugin Distribution - Startup Root Resolution', () => {
   it('MCP startup commands should have config-dir based non-empty fallbacks', () => {
-    for (const relativePath of ['.mcp.json', 'plugin/.mcp.json']) {
+    for (const relativePath of ['plugin/.mcp.json']) {
       const command = mcpStartupCommandFrom(relativePath);
 
       expect(command).toContain('${CLAUDE_CONFIG_DIR:-$HOME/.claude}');