Fix MCP argument contracts and batch limits

[Widthdom]

Summary

• Align MCP tool schemas and validation metadata for aliases, scalar excludePaths, and compatible JSON type hints.
• Report MCP argument clamps/ignored values through warnings and argument_adjustments.
• Add batch_query slot limits, response-budget controls, estimate mode, slot ids, and resumable truncation hints.
• Warn on invalid MCP tool filter names and fail closed for empty explicit allowlists.

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~McpToolContractTests|FullyQualifiedName~McpServerTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~Mcp" (via required Codex adversarial review)
• dotnet run --project tools/CodeIndex.Changelog -- check
• git diff --check origin/main..HEAD
• dotnet format CodeIndex.sln --verify-no-changes
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll index . --json
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• Required Codex adversarial review: No blocking/actionable issues found.

Full dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj was attempted locally earlier but cannot complete in this environment because the installed runtimes do not include Microsoft.NETCore.App 10.0.8-servicing.26229.119, which the current ILLink dependency asks for during publish-trimmed tests.

Fixes #3538
Fixes #3436
Fixes #3539
Fixes #3406