Seems fixed in git-Spigot-2b97a38-95169d4
Deleted all the files for BuildTools and re-built a Spigot jar. Still got git-Spigot-b023457-9d43c91, so it must be latest?
Re-ran BuildTools, Got version git-Spigot-b023457-9d43c91
That isn't latest
<+ThinkBot> Thinkofdeath: You are behind by 6 versions, please rerun BuildTools. (2/4)
This is not fixed 
I've done a clean install with all updated plugins and built a new Spigot jar no older than 10 minutes and the problem still persists.
Did a clean install of everything...
- Vault version 1.5.0-b28 (tried without Vault as well, same result)
- PermissionsEx version 1.23
- CraftBukkit version git-Spigot-b023457-9d43c91
Wiped permissions, removed all other plugins, and then added "minecraft.command.toggledownfall".
Still produced the same error. Without adding the permission node, the error message is "I'm sorry, but you do not have permission to perform this command. Please contact the server administrators if you believe that this is in error." - BTW, misspelling here at "in error" should be "an error".
After adding the permission node "minecraft.command.toggledownfall", I get "You do not have permissions to use this command"
Tried with "bukkit.command.toggledownfall", same result.
I tested with a clean spigot build with only pex installed. So perhaps you should try and figure out which plugin is blocking you.
I tested the permission node "minecraft.command.toggledownfall" with the pex command. It says I do have the permission as well. The message you had is not the same message I get, that message you wrote looks like the NoCheatPlus message you get for blocked commands such as /op and /deop. I get "You do not have permission to use this command.written in light red. I've also tried the override version of the command (/minecraft:<command>). It returns the same error, and as far as I know, no plugin should modify that.
I haven't updated or changed Pex over the restart that caused the problem.
As for plugins blocking the command, these commands have always worked before.
Did you test it while unopped? When opped, all the commands work fine for me.
Just tested and works fine for me.
The full permission node, like stated in the ticket is:
minecraft.command.toggledownfall
However the message when not having the permission node is:
"I'm sorry, but you do not have permission to perform this command. Please contact the server administrators if you believe that this is in error."
Please verify the message and verify you do NOT have a plugin overriding the command.
The bukkit versions of commands were removed in a recent build.
This will be why the change changed recently.
Please test permissions using commands provided by PermissionsEx. Such as /pex user <user> check <permission>. And make sure the player has the permission in all of the worlds. As I recommended before, your best bet for now would be undoing your changes one by one, which can be a time consuming task, but definitely worth it. FYI, spigot doesn't handle permissions, PermissionsEx does. I had a brief look at the recent spigot changes, but I saw nothing that is relating to permissions. PermissionsEx does support world based permissions so make sure you're in the right world when checking permissions.
As in the first post, I tested both bukkit.* and minecraft.*. The old version of Spigot I do not know, the file for the jar itself is 19,517,641 bytes and was installed 12/9/2014 6:08:00 PM EST. PermissionsEx is version 1.22.7-SNAPSHOT (before and after restart), Multiverse-Core is version 2.5-b687 (before and after), Citizens is 2.0.14-SNAPSHOT (before: http://ci.citizensnpcs.co/job/Citizens2/1190/, after: https://dl.dropboxusercontent.com/u/54130586/citizens-2.0.14-SNAPSHOT.jar [From mcmonkey4eva - a Citizens2 dev])
I highly doubt updating Citizens or adding a new world affects how Spigot handles permissions. I know the permission node works, and that it has nothing to do with a failure to properly setup permissions.
https://www.dropbox.com/s/cwmzn9f1bao7wtc/Permissions%20Proof.png?dl=0
^ To confirm permissions are setup correctly (as checked with CommandBook)
I have tested some of the vanilla commands. Unless I have OP, the only commands I can use are list, me, tell, and trigger.
Maybe this problem is related to SPIGOT-183, and may be a side-effect of a bug in the process of fixing that issue, or am I the only one that's having this problem?
Consider testing the bukkit prefix instead of minecraft. And give yourself both perms just to be sure. If that does not work, undo your changes one by one and see what does work. Again, please provide details, you updated spigot, but what was your old version, what's your new version, same goes for everything else, Pex, multiverse, citizens.
I am using PermissionsEx, so wildcards and regex matching work (and I said above that I tested to make sure the permission node was being applied to my permissions). The only thing I changed over the restart, besides updating Spigot, was updating Citizens 2 and adding a new world with Multiverse, but I don't think that should have affected anything.
What have you changed before the restart? What permissions plugin are you currently using? Does it support wildcard (PermissionsEx does, zPermissions does not)? If it does not, then you can't simply have minecraft.*. Details really matter when reporting an issue, please provide them next time.
Just as a note, it worked about an hour ago on a build no older than a day, but then I updated Spigot and it seemed to have broken it when I updated to the most recent.
Edit: None of the vanilla commands work
I have both minecraft.* and bukkit.*.