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>

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}');