fix: MCP servers belong in ~/.claude.json not settings.json

Claude Code reads mcpServers from ~/.claude.json (global state file),
NOT from ~/.claude/settings.json. The settings.json mcpServers key is
silently ignored for MCP loading. Using claude mcp add --scope user
writes to the correct file.

Also document correct registration commands and scope semantics in
RUNTIME.md so agents and users know how to add MCPs that actually load.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

runtime/claude/settings.json

@@ -236,14 +236,5 @@
     "cpan",
     "nohup"
   ],
-  "enableAllMcpTools": true,
-  "mcpServers": {
-    "sequential-thinking": {
-      "command": "npx",
-      "args": [
-        "-y",
-        "@modelcontextprotocol/server-sequential-thinking"
-      ]
-    }
-  }
+  "enableAllMcpTools": true
 }