docs: update docs for 0.3.6

[ishymko]

Description

1. Update README.md, sample agents and sample CLI to use new APIs introduced in refactor: extract request handlers from A2AExpressApp #162 (extract middlewares from A2AExpressApp) and feat: introduce transport agnostic client #198 (transport-agnostic client).
2. Mark A2AExpressApp and A2AClient as deprecated.
3. Ensure samples and TCK import via index files only to "test" that all required types are exported.
4. Consolidate all @example tags to use ```ts.