First of all, there is nothing wrong with using the framework if it does not introduce unnecessary complexity and / or performance penalties for small applications. In PHP, Symfony and Laravel schemes are pretty good in this regard.
Having said that, if you really do not want a “foreign” structure, you still write your own. So it’s better to plan this. Just grab your favorite framework and structure your project exactly as you would when using this framework . Then write the glue code (i.e., your own mini-frame) yourself. If you notice that your project is growing more than expected, you will not have problems with the transition to a "real" structure.
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