What ~/.config refers to and how to put files there?

~ is your home directory, usually /home/username. A file or folder name starting with a . is the Linux version of a hidden file/folder. So ~/.config is a hidden folder within your home directory. Open up your file browser to your home folder, then find the option to show hidden files and folders. If you don't see .config, you'll have to create it. Then navigate into it, find or create the geany folder, go into that, then find or create a folder named filedefs. You can then put the relevant files into there.

.config is a convention, defined by XDG Base Directory Specification see also https://stackoverflow.com/questions/1024114/location-of-ini-config-files-in-linux-unix

~/.config is the directory .config within your home directory (~ is shorthand for that directory).