You should be able to type ç the way I described for all apps, so you could just remove your custom layout. I highly recommend the English (intl., with AltGr dead keys) layout, it’s perfect for coding and writing in English. It’s a bit more work to write in Portuguese, though, so it took me a while to get used to it, but it’s worth it if coding is what you’re doing most of the time. In this layout, you must hold AltGr to get the dead keys, otherwise it’s a normal English layout.
You can also use two layouts — one for English/coding, one for Portuguese — and the keyboard shortcut Super+Space to switch between them. I always have two layouts setup like this, but I never switch anymore because I just learned to love the English (intl., with AltGr dead keys) layout — and I don’t write much Portuguese nowadays.