Fix database metadata and validation issues

[Widthdom]

Summary

• Make metadata writes best-effort when codeindex_meta is absent.
• Add metadata policy stamping and safe pruning of known deprecated null keys while preserving unknown future stamps.
• Re-check column existence after acquiring the migration write lock for standalone ALTER TABLE flows.
• Validate query and batch --db inputs before opening readers on empty/wrong-schema SQLite files.

Validation

• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedNameSetMeta_MissingMetaTable|FullyQualifiedNameInitializeSchema_PrunesKnownDeprecatedNullMetaKeys|FullyQualifiedNameEnsureColumn_RechecksAfterImmediateLockBeforeAlter|FullyQualifiedNameTryMigrateForRead_ConcurrentLegacyMigrations|FullyQualifiedNameWithDb_EmptySqliteFileRejectedBeforeQuery|FullyQualifiedNameRunBatch_EmptySqliteFileRejectedBeforeQuery" -p:UseSharedCompilation=false
• dotnet build CodeIndex.sln -c Release -p:UseSharedCompilation=false
• dotnet run --project tools/CodeIndex.Changelog -- check
• codex adversarial review: No blocking/actionable issues found.

Changelog

• changelog.d/unreleased/1988.fixed.md
• changelog.d/unreleased/2025.fixed.md
• changelog.d/unreleased/2026.fixed.md
• changelog.d/unreleased/2037.fixed.md

Follow-up candidates

• None.

Fixes #1988
Fixes #2025
Fixes #2026
Fixes #2037