I upgraded to macOS Sequoia to try and fix an issue (which it didn't') but introduced some new issues. One of those issues was Apple now tried to stop some of my personal .command scripts from running.

I found a recipe I on Apple Discussions which ran:

• Open up System Settings
• In System Settings, navigate to Privacy & Security. Leave Window Open in the Background
• Open up Terminal (as separate window). DO NOT CLOSE System Settings
• In Terminal, run sudo spctl --master-disable --> Type Password --> Click Enter
• In System Settings, navigate out of Privacy & Security Page (For Example -- Click on Lockscreen), then navigate back to Privacy & Security
• In System Settings --> Privacy & Security Page --> Scroll Down to bottom --> Select Allow Application From --> Select Anywhere (the option will now appear) --> Type Password

To do this will disable security to some extent. So doing it one by one seems safer.