When migrating data from another Mac using Migration Assistant, you can move all Applications or none at all. You can choose the specific folders and all the content within the folder will move over. If you put your previous Mac into Target Disk mode and your old Mac should show up in Finder as an external Hard Drive. Then you can pick and choose what you want to transfer. Some apps need to be moved over using migration assistant while others are stand-alone and can be dragged and drop to your Application folder. The best example of this is when you installed an app, if it goes through an installer, then it will either transferred through migration assistant or just installed again on your new Mac. Check out the articles below for more information about transferring data from one Mac to another.