mcp: add Capabilities fields to ServerOptions and ClientOptions (#713)

This allows users to configure default capabilities, disable defaults,
or suppress listChanged notifications by setting ListChanged: false.

Key changes:
- Add ServerOptions.Capabilities and ClientOptions.Capabilities fields.
- Merge user-provided capabilities with dynamically-added ones (tools,
  prompts, resources, sampling, elicitation).
- Check ListChanged before sending list-changed notifications.
- Deprecate HasPrompts, HasResources, HasTools on ServerOptions.
- Remove unreleased ElicitationModes field from ClientOptions.
- Add clone methods to capability structs using shallowClone helper.
- Add synctest-based tests for notification behavior (go1.25).
- Add TestClientCapabilitiesOverWire and TestServerCapabilitiesOverWire
- Document the new Capabilities API in docs/

Updates #706

internal/docs/rough_edges.src.md

@@ -35,3 +35,12 @@ v2.
 
   **Workaround**: use `ClientCapabilities.RootsV2`, which aligns with the
   semantics of other capability fields.
+
+- Default capabilities should have been empty. Instead, servers default to
+  advertising `logging`, and clients default to advertising `roots` with
+  `listChanged: true`. This is confusing because a nil `Capabilities` field
+  does not mean "no capabilities".
+
+  **Workaround**: to advertise no capabilities, set
+  `ServerOptions.Capabilities` or `ClientOptions.Capabilities` to an empty
+  `&ServerCapabilities{}` or `&ClientCapabilities{}` respectively.