Migrate off the deprecated MCP Roots, Sampling and Logging features and adopt per-request log levels

Documented steps

1. Read https://modelcontextprotocol.io/specification/2026-07-28/deprecated — the deprecated-features registry, introduced with the feature lifecycle policy (SEP-2596).
2. Confirm the state: Roots, Sampling and Logging are all Deprecated as of 2026-07-28 under SEP-2577, with earliest removal being the first revision released on or after 2027-07-28 (a minimum twelve-month window).
3. Replace Roots: pass directories or files via tool parameters, resource URIs, or server configuration instead of asking the client for roots.
4. Replace Sampling: integrate directly with an LLM provider API from your server instead of asking the client's model to generate for you.
5. Replace Logging as a protocol feature: write to stderr on stdio transports, and use OpenTelemetry for observability.
6. If you still emit protocol log messages, read the level per request from _meta['io.modelcontextprotocol/logLevel'].
7. Do not emit notifications/message for a request that omitted that field — the spec states the server MUST NOT.
8. Send notifications/message only on the response stream of the request that set the level, before that request's final response. The server MUST NOT deliver it on a subscriptions/listen stream or any other stream.
9. Reject an invalid log level with -32602 (Invalid params); use -32603 for internal errors.
10. Remove logging/setLevel, ping, and notifications/roots/list_changed — all three were removed in this revision.
11. For tracing instead of logging, propagate OpenTelemetry context through _meta using the unprefixed keys traceparent, tracestate and baggage (SEP-414).
12. Also stop using includeContext values 'thisServer' and 'allServers' — omit the field or use 'none'. They are Deprecated and will be removed no later than Sampling itself.
13. Verify: confirm no notifications/message is emitted for a request without logLevel, and that your traces carry traceparent end to end.