Extract SQLite migrations into separate files (bd-fb95094c.7)

- Created migrations/ subdirectory with 14 individual migration files
- Reduced migrations.go from 680 to 98 lines (orchestration only)
- Updated test imports to use migrations package
- Updated MULTI_REPO_HYDRATION.md documentation
- All tests passing

internal/storage/sqlite/migrations/003_composite_indexes.go

@@ -0,0 +1,30 @@
+package migrations
+
+import (
+	"database/sql"
+	"fmt"
+)
+
+func MigrateCompositeIndexes(db *sql.DB) error {
+	var indexName string
+	err := db.QueryRow(`
+		SELECT name FROM sqlite_master
+		WHERE type='index' AND name='idx_dependencies_depends_on_type'
+	`).Scan(&indexName)
+
+	if err == sql.ErrNoRows {
+		_, err := db.Exec(`
+			CREATE INDEX idx_dependencies_depends_on_type ON dependencies(depends_on_id, type)
+		`)
+		if err != nil {
+			return fmt.Errorf("failed to create composite index idx_dependencies_depends_on_type: %w", err)
+		}
+		return nil
+	}
+
+	if err != nil {
+		return fmt.Errorf("failed to check for composite index: %w", err)
+	}
+
+	return nil
+}