Fix read-only SQLite database handling

[Widthdom]

Summary

• Added --read-only / --immutable query database opens via SQLite immutable read-only URIs.
• Checkpoint WAL before read-only fallback and expose fallback/checkpoint diagnostics in status JSON.
• Restrict POSIX database, WAL, and SHM files to 0600 and expose db_file_mode.

Validation

• dotnet build
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedNameQueryCommandRunnerTests.RunStatus_ReadOnlyFlagOpensImmutableUriAndReportsModeFields|FullyQualifiedNameIndexCommandRunnerTests.Run_ReadOnlyFlag_ReturnsUsageError|FullyQualifiedNameDatabaseTests.DbContext_NewDatabaseRestrictsFileModeOnPosix|FullyQualifiedNameJsonOutputSnapshotTests.RunStatus_JsonOutput_MatchesGolden|FullyQualifiedName~CliFlagSchemaTests"
• dotnet test was attempted, but existing Git commit signing configuration failed Git-based tests with an SSH signing-key passphrase error.

Documentation and changelog

• Updated DEVELOPER_GUIDE.md.
• Added changelog.d/unreleased/1730.added.md.
• Added changelog.d/unreleased/1794.security.md.
• Added changelog.d/unreleased/1798.fixed.md.

Follow-up candidates

• Full repository index can time out near the final extractor files #2711

Fixes #1730
Fixes #1798
Fixes #1794