Atom's Safe Mode, which can be activated by completely exiting all instances of Atom and launching it again using the command atom --safe from the command line, does the following:
~/.atom/packages or ~/.atom/dev/packages
init.coffee
The intent of Safe Mode is to determine if a problem is being caused by a community package or is caused by built-in functionality of Atom. Disabling the init script was added because people tend to use the init script as a mini-package of sorts by adding code, commands and other functionality that would normally be in a package.
For more information on Safe Mode, check the debugging section.