I have been using
apm develop <package_name>
This will work for find-and-replace and the rest of the default. This gives you nice coffee and links everything very nicely. Probably one of my favorite features of Atom. The docs below should mention atom -d IMO (I use that instead)
apm help develop
Usage: apm develop <package_name> 
Clone the given package’s Git repository to the directory specified,
install its dependencies, and link it for development to
If no directory is specified then the repository is cloned to
~/github/<package_name>. The default folder to clone packages into can
be overridden using the ATOM_REPOS_HOME environment variable.
Once this command completes you can open a dev window from atom using
cmd-shift-o to run the package out of the newly cloned repository.
–help, -h Print this usage message