feat(core): MCP server instrumentation without breaking Miniflare

[betegon]

Different approach from #16807 .

Using Proxy was causing issues in cloudflare #16182.

Now using fill we shouldn't have those problems as fill doesn't create a new wrapper object with a different identity, so now:

1. fill just replaces the method on the existing object
2. The transport object keeps its original identity
3. When transport.start() runs and accesses private fields, this is still the original transport object
4. The WeakMap recognizes it as the same object that owns the private fields