All software is held together with patches, shortcuts and cruft.
(Many old houses are as well).
Don’t be surprised. Expect it.
At some point, you’ll need to take a deep breath and pay a bunch of money to start fresh. And then, the very next day, there will be paper clips and string accumulating again.
That’s how it works. And it’s a miracle that it works at all.
(In fact, architecture, design, all the corners of our culture–it’s an evolving process, with cobwebs, repavings, repairs, potholes and improvements. We’d like to believe in the shiny perfect thing, but it’s rare indeed. Even your smartphone has the wabisabi of unused apps and bugs to be avoided.)