Growing a project from one shot mindset prototyping is really problematic. Every time I wish I started by using a real project structure and design philosophy.
And then every time I actually start a project with a real project structure and design philosophy, it goes nowhere and I wish I hadn't wasted the time. Or best case, it's used by a few people internal to whatever company is currently employing me, and security doesn't really matter.
The tech industry is shaped like a funnel, with lots of raw, bad ideas at the top and a few smash mega-hits at the bottom. 99% of the ideas at the top are bad; investing more time than is necessary to prove them out is a mistake. 100% of the ideas that make it to the bottom wish that they'd spent more time designing things at the top. But y'know, if they'd actually done that, they wouldn't have made it to the bottom, they'd be outcompeted by the guy who got a quick and dirty prototype up, made his users happy first, and then closed the gaping security holes (hopefully!) before anyone noticed.
The balance is whatever works, gets people using the product, and ideally keeps them happy.
The balance is generally far more on the quick 'n dirty side than most engineers (myself included) would prefer, but we could look at this as a cognitive bias of engineers rather than a failing of nature.
Once it gets to a certain level of "no longer prototype", it can help if you then start VCS fresh by initing a new git repository. You lose the prototyping history, but you probably won't need it anyway.
