Describe the bug
Protocol class currently hooks onto transports by completely overwriting them, which causes the originally hooked functions to be lost and not executed.

For example this code snippet in the README.md wouldn't be executed.
https://github.com/modelcontextprotocol/typescript-sdk/blob/main/README.md?plain=1#L258-L262

Expected behavior
Hooks on transports should be respected and preserved, allowing original hooked functions to run.

Additional context
The related PR #477 has been open for a while.