Ok, so I can get the 'run' and 'attack' commands to do what they're supposed to by doing this:

 public void combat(){
    System.out.println("Type 'attack' to attack the opponent, and 'run' to run away from combat.");
    input = new Scanner(System.in);

    while(opponent1.isAlive() && player1.isAlive()) {
        if(input.hasNext("run")){
            run();
            break;}

// else if(input.hasNext("attack")) { else if(input.hasNext("attack")) { //Player attacks opponent opponent1.changeHealth(-attack(opponent1.getName())); System.out.println("Player attacks opponent. Opponent's health is now: " + opponent1.getHealth()); System.out.println(); input.next();

            //Checks if opponent is dead
            if (opponent1.isAlive() == false) {
                System.out.println("You won the fight! Congratulations!");
                break;
            }

            //Opponent attacks player
            player1.changeHealth(-attack(player1.getName()));
            System.out.println("Opponent attacks player. Player's health is now: " + player1.getHealth());
            System.out.println();
            input.nextLine();

            //Checks if player is dead
            if (player1.isAlive() == false) {
                System.out.println("Player died. Game over.");
                break;
            }
        }
    }
}

However, if I do this both the attack and run commands ceases to have any effect. I know I'm probably overlooking something extremely basic here, but I can't figure out what:

public void combat(){
    System.out.println("Type 'attack' to attack the opponent, and 'run' to run away from combat.");
    input = new Scanner(System.in);

    while(opponent1.isAlive() && player1.isAlive()) {
        if(input.nextLine().isEmpty()){
            System.err.println("Type either 'attack' or 'run.");
            input.nextLine();
        }

        else if(input.hasNext("run")){
            run();
            break;}

// else if(input.hasNext("attack")) { else if(input.hasNext("attack")) { //Player attacks opponent opponent1.changeHealth(-attack(opponent1.getName())); System.out.println("Player attacks opponent. Opponent's health is now: " + opponent1.getHealth()); System.out.println(); input.next();

            //Checks if opponent is dead
            if (opponent1.isAlive() == false) {
                System.out.println("You won the fight! Congratulations!");
                break;
            }

            //Opponent attacks player
            player1.changeHealth(-attack(player1.getName()));
            System.out.println("Opponent attacks player. Player's health is now: " + player1.getHealth());
            System.out.println();
            input.nextLine();

            //Checks if player is dead
            if (player1.isAlive() == false) {
                System.out.println("Player died. Game over.");
                break;
            }
        }
    }
}