nyxt: update config

package: Remove sqlite version

package: Remove calibre

system: Modify the GDM configuration.

emacs: Add js-indent-level value.

package: Add emacs-ruby-mode.

taix: Add emacs-ruby-mode.

package: Add emacs-debbugs.

package, emacs: Move from lsp-mode to eglot.

package: Add direnv.

emacs: Enable fido-vertical-mode.

emacs: Load custom.el.

package: Remove packages for Nyxt.

emacs: Add configuration to load private.el.

package: Add emacs-esa.

taix: Add emacs-esa.

emacs: Add kintai.el customization.

emacs: Add the PAGER environment variable.

system, package: Move tzdata from the user profile to the system.

channel: Remove flat channel.