MCP tools registered twice when plugin has .mcp.json in both cache and marketplace directories

Bug Description

When a plugin provides an MCP server via .mcp.json, its tools are registered twice in the deferred tools list — once from the installed plugin cache and once from the marketplace source directory. This results in duplicate tool sets with different naming prefixes.

Reproduction

1. Install any MCP-providing plugin from a marketplace (e.g., context7, serena, playwright)
2. Observe the deferred tools list in a new session
3. Each MCP server's tools appear twice:

• mcp__plugin_context7_context7__resolve-library-id (from cache)
• mcp__context7__resolve-library-id (from marketplace source)

Root Cause

Each MCP-providing plugin has two identical .mcp.json files on disk:

| Location | Example Path | Tool Prefix |
|----------|-------------|-------------|
| Installed cache | ~/.claude/plugins/cache/claude-plugins-official/context7/<version>/.mcp.json | mcp__plugin_context7_context7__* |
| Marketplace source | ~/.claude/plugins/marketplaces/claude-plugins-official/external_plugins/context7/.mcp.json | mcp__context7__* |

The files are byte-for-byte identical. Claude Code appears to scan both directories for .mcp.json files, causing each MCP server to be loaded twice.

Affected Plugins

All marketplace plugins that include .mcp.json:

• context7 (2 tools × 2 = 4 deferred tool entries)
• serena (~30 tools × 2 = ~60 deferred tool entries)
• playwright (~25 tools × 2 = ~50 deferred tool entries)
• github (has .mcp.json in both locations)
• greptile (has .mcp.json in both locations)

In total, ~80 duplicate deferred tools are registered.

Impact

• Tool search pollution: ToolSearch returns duplicates, making it harder to find the right tool
• Potential resource waste: Two MCP server processes may be spawned per plugin
• User confusion: Unclear which prefix to use (mcp__plugin_X_X__* vs mcp__X__*)

Expected Behavior

Only the installed (cache) copy of .mcp.json should be loaded for active MCP server registration. The marketplace source directory should be treated as a template/source, not scanned for active servers.

Environment

• Claude Code with plugins enabled
• macOS (Darwin 25.2.0)
• Marketplace: claude-plugins-official

Workaround

None that persists. The marketplace .mcp.json files are git-managed and return on marketplace updates. Deleting cache copies breaks plugin installation.