[BUG] Non-plugin MCP servers: tools not registered in Claude's available tools list

Summary

When adding an MCP server via claude mcp add (non-plugin), the server connects successfully but its tools are not registered in Claude's available tools list. This prevents Claude from calling the MCP tools directly.

Steps to Reproduce

1. Build an MCP server that exposes tools (e.g., skrills with 22 tools)
2. Add it to Claude Code:

``bash
claude mcp add skrills -s project -- /path/to/skrills serve
``

1. Verify server is connected:

``bash
claude mcp list
# Shows: skrills: /path/to/skrills serve - ✓ Connected
``

1. Start a Claude session and check available tools

Expected Behavior

Tools should appear as mcp__skrills__validate-skills, mcp__skrills__analyze-skills, etc. (similar to how plugin MCP servers expose tools like mcp__plugin_sentry_sentry__find_organizations)

Actual Behavior

• Server shows as "Connected" in claude mcp list
• Server appears in session init: "mcp_servers":[..., {"name":"skrills","status":"connected"}]
• BUT no mcp__skrills__* tools appear in the tools list
• Claude cannot directly call the MCP tools

Evidence

From session init JSON (via --output-format stream-json --verbose):

"mcp_servers":[
  {"name":"plugin:sentry:sentry","status":"connected"},
  {"name":"skrills","status":"connected"}  // <-- Connected but no tools
]

Tools list shows mcp__plugin_sentry_sentry__* but NO mcp__skrills__* tools.

Workaround

Users can invoke the CLI directly via Bash, but this defeats the purpose of MCP integration.

Proposed Fix

Ensure non-plugin MCP servers register their tools with the naming convention mcp__{server_name}__{tool_name}, similar to how plugin servers use mcp__plugin_{plugin}_{namespace}__{tool_name}.

Environment

• Claude Code version: 2.0.76
• MCP server: skrills (rmcp-based, stdio transport)
• OS: Linux (WSL2)

Related

This may be related to how claude mcp add stores server config vs. plugin MCP servers.