docs: add deprecation callouts for Roots, Sampling, and Logging #3033

Where was this agreed?

Requested by maintainer David Soria Parra as part of preparing the modelcontextprotocol.io documentation for the 2026-07-28 specification release.

Description

The 2026-07-28 spec release deprecates the Roots, Sampling, and Logging features. The learn and debugging docs still present them as current features without deprecation callouts or migration guidance.

Files to update:

• docs/docs/learn/client-concepts.mdx — add deprecation callouts and suggested migrations to the Roots and Sampling sections
• docs/docs/learn/architecture.mdx — mark Sampling and Logging as deprecated in the primitives lists
• docs/docs/tools/debugging.mdx — note the Logging deprecation and reframe guidance around stderr (stdio) plus OpenTelemetry

Part of the 2026-07-28 release documentation tracking (milestone: 2026-07-28 Specification Release).