Fix reference line context upserts

[Widthdom]

Summary

• Key reference_lines by file_id, line, and context so same-line references with different contexts are preserved.
• Replace the destructive reference-line upsert with idempotent insert behavior.
• Add migration coverage for legacy UNIQUE(file_id, line) indexes and writer coverage for distinct same-line contexts.

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~DatabaseTests.InitializeSchema_MigratesReferenceLinesToContextKey|FullyQualifiedName~DatabaseTests.InsertReferences"
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet test
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json

Documentation and changelog

• Added changelog fragment: changelog.d/unreleased/1755.fixed.md
• No documentation changes were needed beyond the changelog fragment because this preserves intended database writer behavior without changing CLI/MCP usage.

Review

• Adversarial review: no blocking/actionable issues found.
• codex exec adversarial review was attempted, but the Codex CLI returned a usage-limit error before producing a review.

Fixes #1755