Repeatedly "trying to add a new helper tool" on each restart for same application(s) Every time I restart my computer, it tries to "add a new helper tool". For instance I have to reinstall shell commands in Atom on every restart, and it prompts with the "An update is ready to install."  But I see this same issue with other programs too.

Atom installs /usr/local/bin/atom -- but then when I restart it's gone.

I get the same thing from MAMP that it "wants to make changes".

And Slack gives me the same thing as Atom on every restart:




  An update is ready to install. Slack is trying to add a new helper tool.
  
  Enter an administrator's name and password to allow this.
  
  Add Helper


Let me know what other information I can give.
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.