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>

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');