If you want to create .mobileconfig profile from a certificate (for example, to import into Munki), you can use Apple Configurator 2 to do so.
If you have your certificate already in your keychain, launch up Keychain Access.app and find the certificate you want to make into a .mobileconfig profile.
Right-click the certificate and select Export NAMEOFTHECERTIFICATE (export it as a .cer).
Then launch up Apple Configuration 2.app.
Select File and then New Profile
Select Certificates and then Configure.
Find and select the certificate you exported earlier.
Select File and then Save.
Pick a filename for your .mobileconfig, which you can deploy however you want (as I previously mentioned, you can import this into a Munki repo).
We ran into a weird situation once, in which a user could not update anything. Trying to update Adobe Flash ended in an immediate error (Application Initialization Error), launching the Mac App Store led to the App Store saying it couldn't be contacted, and Chrome saying it was updated when it was several versions behind. Pretty much anything that had to contact a server for updates... couldn't.
After rebooting, checking for malware, failed proxy connections, and a bunch of other potential issues, we found out that the /System/Library/Keychains folder was empty.
So we copied the contents of that folder from another Mac, and then, magically, everything worked!
Very obscure issue and obscurer solution. Thanks to J. Pruden for finding it!