Stop pid subsystems in the command instead of subsystem

src/org/usfirst/frc/team2059/robot/commands/shooter/ResetLower.java

@@ -21,7 +21,8 @@ public class ResetLower extends CommandBase {
   }
   // Make this return true when this Command no longer needs to run execute()
   protected boolean isFinished() {
-    return mainArm.getBottomPressed();
+    // Stop when either limit switch is hit
+    return mainArm.getBottomPressed() || mainArm.getTopPressed();
   }
   // Called once after isFinished returns true
   protected void end() {

src/org/usfirst/frc/team2059/robot/commands/shooter/ResetUpper.java

@@ -21,7 +21,8 @@ public class ResetUpper extends CommandBase {
   }
   // Make this return true when this Command no longer needs to run execute()
   protected boolean isFinished() {
-    return mainArm.getTopPressed();
+    // Stop when either limit switch is hit
+    return mainArm.getBottomPressed() || mainArm.getTopPressed();
   }
   // Called once after isFinished returns true
   protected void end() {

src/org/usfirst/frc/team2059/robot/commands/shooter/SetArmPosition.java

@@ -27,7 +27,8 @@ public class SetArmPosition extends CommandBase {
   }
   // Make this return true when this Command no longer needs to run execute()
   protected boolean isFinished() {
-    return false;
+    // Stop when either limit switch is hit
+    return mainArm.getBottomPressed() || mainArm.getTopPressed();
   }
   // Called once after isFinished returns true
   protected void end() {

src/org/usfirst/frc/team2059/robot/subsystems/MainArm.java

@@ -31,12 +31,7 @@ public class MainArm extends PIDSubsystem {
     return getDegrees();
   }
   protected void usePIDOutput(double output) {
-    // Only run if neither limit switch is hit
-    if (!calibrate()) {
-      moveArm(output);
-    } else {
-      moveArm(0);
-    }
+    moveArm(output);
   }
   public double getRaw() {
     return pot.getAverageVoltage();