fix: point mcp.json at the real MCP endpoint + replace stale tool docs

- mcp.json: bare https://mcp.spaghetti.gg ->
  https://mcp.spaghetti.gg/api/mcp/agentic-engine/mcp (the host root does
  not serve MCP; Caddy proxies the whole host without a path rewrite)
- SKILL.md/README: replace tools that no longer exist (analyze_crash,
  audit_assets, search_kb) with the shipped set (analyze_logs,
  tidy_assets, make_tool, topup, the five research tools); document
  credit costs and the approval flow
- drop stale claims: GoTrue, spaghetti.gg/dashboard, tm_/prj_ id
  prefixes, '.spaghetti auto-created on first tool call' (unimplemented)
- plugin.json: 0.1.0 -> 0.1.1

mcp.json

@@ -3,7 +3,7 @@
   "mcpServers": {
     "spaghetti": {
       "type": "streamable-http",
-      "url": "https://mcp.spaghetti.gg"
+      "url": "https://mcp.spaghetti.gg/api/mcp/agentic-engine/mcp"
     }
   }
 }