What this will do is create the jsb3 file that will be used to create the build. You point it to your app entry point (usually the index.html) and tell it what to name the jsb3 file. This will go through you app files and parse your requires/uses/views/models/stores/controllers arrays and create a dependency list in the order you need it to be in.
sencha build -p app.jsb3 -d ./
This is what will do the actual combining and minifying of the code based on the jsb3. You give it the name of the jsb3 file and the directory to place the files in.
These two steps could have been combined into one command but the benefit of leaving them separate is that you can edit the jsb3 file that will be used int he 2nd command. You probably won't do it much but it can be useful.