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/013_repo_mtimes_table.go

@@ -0,0 +1,36 @@
+package migrations
+
+import (
+	"database/sql"
+	"fmt"
+)
+
+func MigrateRepoMtimesTable(db *sql.DB) error {
+	var tableName string
+	err := db.QueryRow(`
+		SELECT name FROM sqlite_master
+		WHERE type='table' AND name='repo_mtimes'
+	`).Scan(&tableName)
+
+	if err == sql.ErrNoRows {
+		_, err := db.Exec(`
+			CREATE TABLE repo_mtimes (
+				repo_path TEXT PRIMARY KEY,
+				jsonl_path TEXT NOT NULL,
+				mtime_ns INTEGER NOT NULL,
+				last_checked DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP
+			);
+			CREATE INDEX idx_repo_mtimes_checked ON repo_mtimes(last_checked);
+		`)
+		if err != nil {
+			return fmt.Errorf("failed to create repo_mtimes table: %w", err)
+		}
+		return nil
+	}
+
+	if err != nil {
+		return fmt.Errorf("failed to check for repo_mtimes table: %w", err)
+	}
+
+	return nil
+}