Fix MCP JsonNode clone round trips

[Widthdom]

Summary

• Replaced MCP JsonNode serialize/parse clone paths with a shared DeepClone() helper for response IDs, progress tokens, session capability copies, and structured error extra data.
• Preserved the upstream MCP session capability byte/depth caps by measuring with the bounded JSON writer, checking depth directly, then cloning only the retained diagnostics.
• Added MCP JsonNode cloning should avoid serialize-and-parse round trips #3055 regression tests and a changelog fragment.

Issues

Fixes #3055

Not handled by this PR:

• MCP out-of-band client responses should cap result/error JSON before cloning #3098: resolved and closed upstream while this PR was being conflict-resolved; this branch now inherits the upstream implementation and the final PR diff does not carry a separate MCP out-of-band client responses should cap result/error JSON before cloning #3098 change.
• MCP initialize session metadata should cap clientCapabilities and roots before status exposure #3225: excluded because an existing issue comment said work started on branch fix-issue3225-3076; upstream changes were only merged to resolve conflicts.
• MCP client session capture should cap retained roots and capabilities before status output #3076: excluded because an existing issue comment said work started on branch fix-issue3225-3076; upstream changes were only merged to resolve conflicts.

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~McpServerTests" -p:UseSharedCompilation=false
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• Adversarial review: No blocking/actionable issues found.

Notes

• Changelog fragment: changelog.d/unreleased/3055.fixed.md.
• No AGENT.md, CLAUDE.md, or AGENT_GUIDE.md changes are present in the final PR diff.
• Conflict resolution was done by merging latest origin/main because local rebase/history rewrite was blocked in this environment.