We are all glad you are getting more interested in the sport! I am not going to directly answer the question you asked, because others have. I'm providing some possible other considerations.
Often, it is not objectively worth it to upgrade the components on an entry-level bike. This doesn't mean you should not do so. But rather, it will likely be more cost effective to buy a full bike with the spec you want. That's even more true with used bikes, but as a newer cyclist, you may not exactly know your fit parameters, which can pose an issue buying used.
Manufacturers typically get pretty big OEM discounts. They can get a 105 or whatever groupset a lot cheaper than you can. They mass assemble the bikes at a factory. Whereas you have to buy a groupset at retail, and you either have to DIY the installation, or convince a friend (preferably a skilled one) to help you, or pay a bike shop to install it. And at the end of the day, you'll still have an entry-level frame.
Many cyclists don't appreciate the fact that cables need periodic replacement. It's hard to objectively say how long they should last. I went 3 years before replacing my Shimano Ultegra cables, but that was pushing it, it was a road bike, and those are high-end low-friction cables. It could be that a tune-up will fix your issues with shifting. However, I'm not familiar with the cable routing on your Cannondale. Routing cables internally can put tight bends in them, and shift and brake cables inherently don't like tight bends. If the Topstone's routing isn't good, this may be an inherent problem - however, I simply don't know. You might consider upgrading to good shift housing - Jagwire, a common aftermarket brand, makes good slick cables and housing. I perceive it to not be as good as Shimano's SP41 housing and coated cables, but I am very fussy, and it's really splitting hairs.
You could also upgrade to compressionless brake housing, which can really help with mechanical brakes. However, this is a bit pricey. Also, if the brakes are bad, there may be only so much that good housing can do. I'm not saying the Topstone's brakes are bad. What I am saying is that many lower-level mechanical disc brakes don't have that much power. This may stem from the caliper design, or from the pads (which you could also upgrade), or from cheap housing, or from poor routing (which can't be fixed).
Thus, getting a tune up with more premium cable and brake housing may also pose a sticker shock. However, do appreciate that complex mechanical objects inherently require ongoing maintenance. Could we make reduce maintenance requirements for bicycles? Yes, but the tradeoffs might not be worth it. For example, we have electronic shifting, and even the entry level groups cost a lot (e.g. 105 Di2 is something like 3x the price of the previous generation mechanical 105). We have hydraulic brakes where the system is completely sealed from contamination, but these do require periodic bleeds, and that is a more complex task than replacing housing, plus they are more expensive.
What can we do with entry-level bikes we've outgrown? Common options include turning them to commuters, or selling or passing them on to another new cyclist. If you sell, do be aware that bikes depreciate a lot, so I'm aware that this will be yet more sticker shock.