Performed upgrade on late 2012 mac mini from OS 10.8.5 to 10.11.5 to add Adobe CC 2015 compatibility. Upgraded SF from v5 to v7. Fonts have been pared down per Best Practices, just as I have done many times before on other machines. The new machine shows 154 system fonts active, which I’ve reluctantly come to accept as the new standard (3x more than last OS). What it also shows are 79 other fonts missing from the user/library/fonts folder, all beginning with a period (.Al Bayan, etc.) There are no fonts in the user/library/fonts directory, nor in the /library/fonts directory, only the /system/library/fonts directory. The /library/fonts directory did hold some of those fonts for a short time when /system/library/fonts refused to allow me to remove the unnecessary fonts. Those fonts are now deleted, which I suppose is prompting the missing fonts message.
This machine was so resistant to font removal, more so than an identical machine that went through the same procedure. Still, the other machine does not warn of missing fonts from /user/library/fonts. The new machine seems to be working well, but just keeps reporting those missing fonts rather than updating itself to show no fonts in that directory like past versions of SF did. I have cleared font caches and restarted. I have used TinkerTool System to clear ALL caches (except SIP protected System caches) and restarted. Nothing has prompted SF7 to stop reporting those missing fonts that I don’t want to begin with. Any suggestion on how to stop this behaviour?