You generally don’t want to put data in the ghost installation directory. There’s many ways you can set up your Ghost environment for theme development.
The one I use involves a directory for the theme contents, and a subdirectory specifically for ghost. I then use a symlink to map the built theme’s directory (since my themes have a build process) to instance/content/themes/theme-name
Another common choice is to create the theme in content/themes/theme-name and work from there.
Looking at the output of ls -al, there’s a .idea directory which isn’t permitted. You can install ghost in a subdirectory with the -d flag (e.g. ghost install local -d instance)