Another great way to learn what goes into an MVC framework and how things work is to try rebuilding parts of an existing framework. This will both help learn how the framework you want to use works while guiding you through how to create your own. When you get stuck on your own framework or want to see how they did something you really like you can jump into the framework's source code to see how it works.
One huge thing I would recommend, especially for beginners, is to not use your own framework for a production site that is important. The pre-built frameworks handle a lot of security concerns most beginners aren't going to be familiar with and may not be able to keep up with the latest threats at the speed a mature framework can.
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Another great way to learn what goes into an MVC framework and how things work is to try rebuilding parts of an existing framework. This will both help learn how the framework you want to use works while guiding you through how to create your own. When you get stuck on your own framework or want to see how they did something you really like you can jump into the framework's source code to see how it works.
One huge thing I would recommend, especially for beginners, is to not use your own framework for a production site that is important. The pre-built frameworks handle a lot of security concerns most beginners aren't going to be familiar with and may not be able to keep up with the latest threats at the speed a mature framework can.