Repeatedly "trying to add a new helper tool" on each restart for same application(s)

Try changing the ownership of Atom.app. In my case, Atom.app was found in /Applications, and ownership was:

drwxr-xr-x   3 1699963712  365896978    102 Dec  8 12:48 Atom.app

I ran the following command:

sudo chown -R $USER:wheel /Applications/Atom.app

In my case, any program with ownership of root or the numeric code listed above would have a popup a few seconds after opening. Changing ownership of the .app directory corrected the behavior and I don't see it anymore.

I found the information at this site.

Searching for the application and manually dragging it into the Applications folder also worked for me.

Here's my solution: run any OS X atom-based apps such as Slack or Signal out of your ~/Applications directory.

The root of the problem is that these apps were installed system-wide via a mechanism like Homebrew, or manually by you and owned by root. So the easy/quick workaround is to copy them to a place where your current user has write access:

killall Slack && rsync -av --delete /Applications/Slack.app/ ~/Applications/Slack.app/ && open ~/Applications/Slack.app

Now when the atom application's built-in update mechanism tries to write to its files, it can! No more annoying pop-up windows!