I still seem to have fonts missing, some weights in a family etc.
The first would be caused by duplicates. In other words, font conflicts which cause the conflicting font, or both, to disappear.
I seem to have masses of duplicates too.
The duplicates were caused by the Safe Mode boot to reset Font Book's database. Doing that enables every font on the system (in the three main Fonts folders). So any conflicts you had resolved before are now conflicting again. Unfortunately, the only way to fix a mangled Font Book database is a Safe Mode boot.
Do i need to pile all fonts into one folder...system or user library fonts?
The System folder is a not a good place to put your fonts for at least a couple of reasons. One, it's a pain in the rear. You have to enter your admin password just to put them in there. Then again to
delete them from the folder since you can't simply drag them back out. Secondly, if you put conflicting fonts into that folder, the only way to resolve it is to manually delete one of the fonts.
The following files can no longer be found but contain fonts used by one of your defined font libraries.
It's complaining about fonts that are listed in one or more font collection files (found in your user account) aren't on the drive where they were at the time the collections were created.
The short answer. Get rid of Font Book and spend the money on a font manager that actually works. Suitcase Fusion 3 or FontExplorer X Pro are currently the best choices. Long answer, follow these steps:
1) Open Font Book, and then its preferences. Uncheck the box for "Alert me if system fonts change". Close the preferences and shut down Font Book. Put the Font Book application in the trash and delete it.
2) Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding it until OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally.
This will reset Font Book's database and clear the cache files in your user account. Any font sets you have created will be gone. Also, all fonts in the three main Fonts folders (System, Library, your user account) will now be active, regardless of their state beforehand.
The main goal in step 2 is to remove the orphaned Font Book database from the hard drive. With the Font Book application no longer on the hard drive, a new one cannot be created. Which is what we want.
3) Follow the
Font Management in OS X guide to get your fonts down to the minimum. The /Library/Fonts/ folder, and the Fonts folder in your user account should be empty. Put them wherever you want to use when needed, just not in any other Fonts folder. You will never put any fonts in these two folders again. The only fonts remaining in the /System/Library/Fonts/ folder should be:
AppleGothic.ttf
Geneva.dfont
HelveLTMM
Helvetica LT MM
Helvetica.dfont
HelveticaLight.ttf
HelveticaLightItalic.ttf
HelveticaNeue.ttc
Keyboard.ttf
LastResort.ttf
LucidaGrande.ttc
Menlo.ttc
Monaco.dfont
Times LT MM
TimesLTMM
Times.dfont
Symbol.dfont
If you need to use other versions of Helvetica, Helvetica Neue or Helvetica Light, you'll have to move those to another location (with the rest of your third party fonts) and delete the duplicates in the ProtectedFonts folder so they can't put themselves back.
These should be the only permanently active fonts left on the drive.
4) Purchase Suitcase Fusion 3 or FEX Pro and install
one or the other. Both have trial periods to test them and see which you prefer. If you decide you want to try both, make sure to completely uninstall the first before installing the second. Never have more than one font manager on your system at a time.
No matter which one you choose, make sure the option to activate fonts in place is on. That way they will never be copied anywhere, so the /Library/Fonts/ folder, and the Fonts folder of your user account will always remain empty. There's no need for any fonts to ever be in those folders in order to use them. That's what you use a good font manager for. Turn them on, turn them off, don't copy or move fonts from their original location, ever.
I suggest these two font mangers in particular not just because they work so well, but because both will not let you turn conflicting fonts on, assuming you set up the preferences correctly to begin with. None of the others I've tested work as well as SF3 and FEX Pro.
I may receive some form of compensation, financial or otherwise, from my recommendation or link.