Ubuntu – The use of Hidden folders in home

You should be relatively safe:

• Surely your OS won't break, dot files in home directory are mostly configuration files, if they're not there any app will just use the defaults.
• Device drivers (as ethernet,video,sound,...) should be configured systemwide, so you should be safe.
• Those are the things will "break" as all your preferences/customizations will get lost, but you don't care ;)

In fact if you add another user to the system his home directory will be mostly empty, apart from some default files which are put inside by default. But those defaults are distro-specific and surely not mandatory.

So yes, you should be quite safe deleting everything under home.

Just in case, play safe and move them to another directory and check everything is ok before deleting them.

You can use gsettings to access the responsible setting in the dconf registry easily from the command line.

The setting whether to show hidden files (with names starting with .) is located in the schema org.gtk.Settings.FileChooser and called show-hidden.

Allowed values are either true (show hidden files) or false (don't show them).

So here are the commands to enable or disable showing the hidden files:

gsettings set org.gtk.Settings.FileChooser show-hidden true
gsettings set org.gtk.Settings.FileChooser show-hidden false

To automatically run this command every x minutes, there are two good resources to learn how to achieve this:

• Using cron (minimum resolution is 1 minute): help.ubuntu.com: Cron How-to

  Note that cron runs tasks with a very limited set of env variables which do not include DBUS_SESSION_BUS_ADDRESS, but that's needed for gsettings to work. So we have to take care of setting this variable ourselves in the script we run if we need it

  I prepared a script for you (with the help of @JacobVlijm who linked me this answer on Stack Overflow by @Radu Rădeanu) that takes care of this problem and can be run directly by cron:

  #!/bin/bash
  
  # --> Script to disable showing hidden files - to be run as cron job <--
  
  # export DBUS_SESSION_BUS_ADDRESS environment variable
  PID=$(pgrep gnome-session)
  export DBUS_SESSION_BUS_ADDRESS=$(grep -z DBUS_SESSION_BUS_ADDRESS /proc/$PID/environ|cut -d= -f2-)
  
  gsettings set org.gtk.Settings.FileChooser show-hidden false
  

• Without using cron: How to execute command every 10 seconds (without cron)?