Fix MCP reader cleanup and error reporting

[Widthdom]

Summary

• Dispose MCP DbReader instances deterministically, including the index-project SQL graph signal reader.
• Report MCP per-file index failures with failed_count, a capped failures list, and global log context.
• Flush stdout/stderr and log MCP loop failures before returning an error exit code.
• Preserve DbDebug row-read exception chains and root-cause reporting.

Validation

• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release -p:UseSharedCompilation=false --filter "FullyQualifiedName~DbDebugTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj -c Release -p:UseSharedCompilation=false --filter "FullyQualifiedName~McpServerTests" was attempted; 424 tests passed per target framework and 7 existing Git-metadata tests failed because local Git commit signing requested /Users/widthdom/.ssh/id_ed25519_signing passphrase in temp repositories.

Documentation and Changelog

• Added changelog.d/unreleased/1714.fixed.md
• Added changelog.d/unreleased/1716.fixed.md
• Added changelog.d/unreleased/1720.fixed.md
• Added changelog.d/unreleased/2010.fixed.md

Review

Adversarial review result: No blocking/actionable issues found.

Follow-up Candidates

• None.

Fixes #1714
Fixes #1716
Fixes #1720
Fixes #2010