Align handwritten SQLite C++ helpers with generated Nitro namespaces #349

PR #298 changes handwritten SQLite helpers to use the namespace generated by Nitrogen and makes hybrid-object includes relative to their owning directory. These changes affect every native platform and deserve a separate review.

Extract the namespace and include changes while preserving #326's connection serialization. Keep the metadata behavior fix in #313. This is related to #332 but does not implement its broader filename-prefix proposal.

Source: #298