Consider SQLite for baseline storage

[bubunyo]

The baseline is currently a single JSON blob. At 5000+ functions this becomes slow to read/write and requires full deserialization even when only a subset of data is needed.

Acceptance criteria

• Evaluate SQLite as an alternative baseline backend
• Key benefits: partial reads (only load hashes for changed files), atomic writes, no serialization overhead
• Implement behind a config flag (e.g., baseline_format: sqlite | json)
• Keep JSON as default for simplicity; SQLite as opt-in for large codebases