How to move lots of dotfiles staying at /home without breaking programs?

With more and more programs installed on my computer, I am tired of seeing lots of dotfiles while I have to access them often. For some reason I won't hide dotfiles when browsing files. Is there a way to move them to a better place I want them to stay (e.g. ~/.config/$PROGCONF) without affecting programs while running?

Symlinks still leave file symbols, which is far from my expectation. I expect that operations like listdirs() won't show the files while opening them uses a redirection.

>"For some reason it won't hide dotfiles when browsing files.":

That depends on the file manager you use. nautilus hides it by default and most file managers have an option to "show/hide hidden files". The ls command by default omits out hidden files (files starting with a dot). It lists all files with the option -a.

>"Is there a way to move them to a better place":

Programs which have support for "XDG user directories" can store their config files in `~/.config/$PROGRAM_NAME/. If the program doesn't support that and expects the config file to be present in the home directory, there is little you can do (Maybe you can give us a list of what programs' config files you want to move). The process differs for each program.

Let me give an example with vim. Its config file is ~/.vimrc. Lets say you move the file to ~/.config/vim/.vimrc. You can make vim read the file by launching vim using the following command.

vim -u ~/.config/vim/.vimrc

You can modify the .desktop entry or create a new shell script to launch vim using the above command and put it inside /usr/local/bin/ or create shell functions / aliases. You can read more about changing vim's config file location in this SO question.

This arch wiki article has application specific information.

>"without affecting programs while running":

It depends on a few factors namely the file system used, the program we are dealing with and so on.

Generally, deleting / moving files only unlinks the file name from an inode and programs read / write files using inodes. Read more here. And most programs read the config file at the start, load the values into memory. They rarely read the config files again. So, if you move your config file while the program is running (assuming the program supports config in both places), you won't see a difference until the program is restarted.

> "I expect that operations like listdirs() won't show the files"

I am assuming you are talking about os.listdir() in python. If files are present, os.listdir() will list them, there is little you can change about that. But you can write custom functions to omit out the hidden files from being listed.
This SO question can help with that.