How to remove security notifications about unapproved software after upgrading to macos High Sierra? Upgrading to High Sierra is really painful. I cannot do brew upgrade, I am getting thousands of security notifications - see the attached file.  There are some recipes in Internet but they are not working, maybe the latest upgrade does not allow them.  I can approve files one by one but there are hundreds of them.  Maybe at least I can approve all files in a directory? Or run a script approving all files?
It appears you have an anti-virus application called Bit9. If it is causing more difficulty than help, you can always deactivate or uninstall it. If this is a institutionally managed machine, contact your system admin or help desk.

If you feel you need to have an anti-virus application, be sure to confirm that it will run correctly with macOS High Sierra. You may need to disable the anti-virus' blocking of scripts if you are intentionally running scripts for what you are doing.