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Add SQLite foundation with connection, PRAGMAs, and goose migrations (#3771)

Introduce pkg/storage/sqlite/ package with:
- db.go: DB wrapper, Open() with PRAGMA config (WAL mode,
  busy_timeout=5000, synchronous=NORMAL, foreign_keys=ON,
  cache_size=-2000), DefaultDBPath() helper
- migrations.go: Embedded SQL migrations using goose v3 Provider API
- 001_create_entries_and_skills.sql: Full RFC-0041 schema (entries,
  installed_skills, skill_dependencies, oci_tags tables)

New dependencies: modernc.org/sqlite (pure Go, no CGo),
github.com/pressly/goose/v3.

Part of #3648, implements #3739.

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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