The release of version 5.28 coincides with the release of TeX Live 2024 and MacTeX-2024, and some changes are related to that release:
TeXShop rewrites the Inactive folder whenever a new version of the program is released, but the rewrite is conservative, updating old files and adding new files and folders. No files or folders are ever removed, so the Inactive folder can become cluttered with irrelevant material. If you want only the latest version of this folder, move the Inactive folder to the desktop (do not move other folders). The next time TeXShop starts, it will recreate Inactive with the current default version.
defaults write LinkPopups NO
Because the auxiliary program is not TeXShop, TeXShop had to find a way to give it the applescript code it should run. Luckily, Unix provides a folder named tmp where programs can store temporary information. So TeXShop put the appropriate applescript program in tmp, and then gave the auxiliary program the name of this file. Since tmp may be used by many programs, knowing the name of the desired file is important.
Then the author of TeXShop (and that would be me) made a stupid mistake. He always used the same name for the applescript file in tmp. As long as the same user ran applescript programs, there was no issue, because each new applescript file in tmp overwrote the previous one. But if a user logged out and then logged in as someone else, the new user did not have permission to overwrite the previous file, so the old file remained and ran.
This is not a subtle mistake and Unix programmers are aghast after reading this explanation. But Simmons taught me an important lesson, and I'm grateful. By the way, it turns out that Apple has its own substitute for tmp and TeXShop now does the right thing. If you are a Cocoa programmer, please don't write me.