The schema_migrations table definition now lives in
internal/database/schema/000.sql instead of being hardcoded as an
inline SQL string in database.go. A bootstrap step checks
sqlite_master for the table and applies 000.sql when it is missing.
Existing databases that already have the table (created by older
inline code) get version 000 back-filled so the normal migration
loop skips the file.
Also deduplicates the migration logic: both the Database.runMigrations
method and the exported ApplyMigrations helper now delegate to a single
applyMigrations function.
Adds database_test.go with tests for fresh migration, idempotency,
bootstrap on a fresh DB, and backwards compatibility with legacy DBs.
Migrations are stored in schema/*.sql and embedded via go:embed.
Applied migrations are tracked in schema_migrations table.
Initial schema includes source_content, source_metadata, output_content,
request_cache, negative_cache, and cache_stats tables.
