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/011_external_ref_unique.go

@@ -0,0 +1,66 @@
+package migrations
+
+import (
+	"database/sql"
+	"fmt"
+	"strings"
+)
+
+func MigrateExternalRefUnique(db *sql.DB) error {
+	var hasConstraint bool
+	err := db.QueryRow(`
+		SELECT COUNT(*) > 0
+		FROM sqlite_master
+		WHERE type = 'index'
+		  AND name = 'idx_issues_external_ref_unique'
+	`).Scan(&hasConstraint)
+	if err != nil {
+		return fmt.Errorf("failed to check for UNIQUE constraint: %w", err)
+	}
+
+	if hasConstraint {
+		return nil
+	}
+
+	existingDuplicates, err := findExternalRefDuplicates(db)
+	if err != nil {
+		return fmt.Errorf("failed to check for duplicate external_ref values: %w", err)
+	}
+
+	if len(existingDuplicates) > 0 {
+		return fmt.Errorf("cannot add UNIQUE constraint: found %d duplicate external_ref values (resolve with 'bd duplicates' or manually)", len(existingDuplicates))
+	}
+
+	_, err = db.Exec(`CREATE UNIQUE INDEX IF NOT EXISTS idx_issues_external_ref_unique ON issues(external_ref) WHERE external_ref IS NOT NULL`)
+	if err != nil {
+		return fmt.Errorf("failed to create UNIQUE index on external_ref: %w", err)
+	}
+
+	return nil
+}
+
+func findExternalRefDuplicates(db *sql.DB) (map[string][]string, error) {
+	rows, err := db.Query(`
+		SELECT external_ref, GROUP_CONCAT(id, ',') as ids
+		FROM issues
+		WHERE external_ref IS NOT NULL
+		GROUP BY external_ref
+		HAVING COUNT(*) > 1
+	`)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	duplicates := make(map[string][]string)
+	for rows.Next() {
+		var externalRef, idsCSV string
+		if err := rows.Scan(&externalRef, &idsCSV); err != nil {
+			return nil, err
+		}
+		ids := strings.Split(idsCSV, ",")
+		duplicates[externalRef] = ids
+	}
+
+	return duplicates, rows.Err()
+}