How do I make an application from scratch?

Start by deciding what you are trying to produce. That can be as simple as "I wanna make a text editor" to a pretty solid idea of exactly what you want to use / sell.

Then decide what environment you want it to work in. It this Cloud based? Web? Windows? iPhone? Android? Linux? The more environments you add, the more complex you are making the job.

Then sit down and write a specification: describe how the app is going to do what it does. This should be reasonably full: It's not a development specification it's a functional spec.

And that provides you with the next two design docs you need: the dev spec, and the test spec. The later is important - it gives you a "end point" for the project, a point at which you can start to consider releasing it.

You can then start using the dev spec to design the actual software ...

And to be honest, I wouldn't start a "modern app" these days from a basis of "C, Python, and Javascript"!