How To Use Debug Mode
If you are having problems with permissions and permission nodes, use the PEX debugging mode to find out what's going wrong. For example, if I attempt to use the command /fly which is given to GroupA by plugin B, and the command does not work, I would follow this process:
1. Type pex user Stormbow toggle debug into the console to turn on debug mode.
2. Have Stormbow type /fly in-game while Stormbow is in GroupA.
3. Type pex user Stormbow toggle debug into the console to turn off debug mode.
4. Look through the console output and find out which permission node GroupA does not have.
5. Add the missing permission node to GroupA.
6. Return to step 1 (above) and test the /fly command again.
If you have used this procedure correctly and you're unable to comprehend the console output in step 4, return to your own thread on this forum to share the output with me. (You can copy it to a text file and attach it to your post, or you can Pastebin it and leave me the link.) I'll take a look at it for you as soon as I'm available.
Stormbow AuthorThe intent of this guide is to give users a solid list to work with when trying to resolve just about any problem they could run into when running a Minecraft server with PEX.
--------------------------------------------------As of Minecraft 1.9, every group must have an inheritance section, even if there is no group to inherit from. See line 19 of the example for how to give a group an inheritance section with no group listed.
A command list and more details about Inheritance can be found right here.
--------------------------------------------------One of the best permissions you can give to yourself, as the server owner, is permissions.* because this will ensure that you have access to all of the PEX commands, no matter which group you are in while you're setting up, debugging, and otherwise troubleshooting your server.
Type the following into your console (using your usersname, not mine) to give yourself this permission:
--------------------------------------------------Don't use "OP". It can make you think things are programmed correctly on the server when they really are not. The "OP" feature was intended for Vanilla servers that do not use any plugins or mods at all.
--------------------------------------------------• Be sure that your plugins are for your version of Minecraft. This means reading the release notes on every plugin that you download. Just because the homepage of the plugin says the plugin is for Minecraft X.Y.Z, doesn't mean it actually is. Those homepage version numbers are often restricted to a few selections in a drowndown list, and authors can't select the true version for the plugin.
--------------------------------------------------• Always assume that a plugin for Minecraft verision A.B.C will not work in Minecraft A.B.D. Test the plugin thoroughly before continuing on with your server setup. You don't want a dozen plugins malfunctioning and giving you problems at the same time. This makes your overall problem solving less confusing and easier to complete.
--------------------------------------------------• If it ain't broke, don't fix it. The default settings in many Minecraft and plugin files are fine for most servers. Do Not change any settings anywhere until you absolutely know what the setting does, what changing it will do, and what your options are for changing the setting. This is most commonly a problem for people who change the server.properties file spawn-protection to anything higher than 0. This setting, when higher than 0, prevents people from building (and more) near the server's spawn location. With the myriad of other protection plugins in use, this setting is obsolete and should remain at 0. Also common, people make changes in the PermissionsEx\config.yml file which do not need to be changed. Your config.yml file should look like this example as of Minecraft 1.7.9. Anyone who is getting their files from unofficial sources (such as non-PEX forums and other Minecraft websites) should expect those files to be grossly outdated and dysfunctional.
--------------------------------------------------• Follow this example for basic server permissions.yml setup, and this example for multiworld server permissions. Many people in the past few months are putting the "options:" settings (such as "default: true" and prefixes) outside of the "options:" section, and PEX does not function properly.
--------------------------------------------------• Follow the Basic PEX Tutorial and PEX Prefix/Suffix Guide if you are having problems setting up groups, permissions, or prefixes. These 2 guides are likely to answer most of your questions and solve many of your problems. A chat management plugin is absolutely required to get prefixes/suffixes to display in-game.
--------------------------------------------------• If you want Prefixes and Suffixes to display in-game, you must have a chat management plugin. You're on your own to find a chat management plugin that you like, now that EssentialsChat (and the Essentials bundle) is no longer being supported and updated by the original author. EssentialsX from Spigot has many problems, and should not be considered functional on your server until you have thoroughly tested all of the more than 400 permission nodes which came in the original Essentials package. I have written up a Basic Prefix/Suffix Tutorial to help you out in this area.
--------------------------------------------------• Always run your permissions.yml file through an Online YAML Checker, especially after making major changes such as adding a group. This will give you a very good indicator of where your problems are within the permissions.yml file. By following the permissions.yml example (linked 3 sections above), and referencing the error shown in the Checker, you can typically find problems and solve them very quickly. Check your file after every group you add to the server, so you don't have 10,000 lines to search through and fix problems in.
--------------------------------------------------• If you don't have it already, I highly recommend you get
Notpad++to edit all of your permissions.yml and other Minecraft files. It will show you line numbers to help you find the errors mentioned above.--------------------------------------------------• Do not use the tab key, ever, in YAML files (such as the permissions.yml file for PEX). This will always cause fatal errors and PEX will not function, showing up red in-game in the plugins list.
--------------------------------------------------• Vanilla Permissions should not be considered functional until fully tested on your server. Many, many times in the past year (and counting) that I have been helping people on this official PEX forum, I have seen problems with these permissions.
For example: there can be 2 Minecraft 1.7.9 servers run by 2 different players, on 2 different server hosts, and one will have full functionality and control of these permissions while the other player has no control over them. It is also possible to have only partial control of these permissions. Sometimes server owners can give these permissions out; sometimes server owners can not give these permissions out; sometimes server owners can negate these permissions; sometimes server owners can not negate these permissions. Even when these permissions are not given to players
--which means the players can not use the commands--the commands have still been accessible. I have tried on multiple occasions to find out why this is, but my countless hours of testing have not been able to recreate the problem and the powers that be have never replied to me when I've asked them what was going on here. On my 1.7.2 server, no permissions were given out, and most commands were still accessible by all groups on the server (even when their equivalents from Essentials were negated as well).--------------------------------------------------• If you are having problems with permissions and permission nodes, use the PEX debugging mode to find out what's going wrong. For example, if I attempt to use the command /fly which is given to GroupA by plugin B, and the command does not work, I would follow this process:
1. Type pex user Stormbow toggle debug into the console to turn on debug mode.
2. Have Stormbow type /fly in-game while Stormbow is in GroupA.
3. Type pex user Stormbow toggle debug into the console to turn off debug mode.
4. Look through the console output and find out which permission node GroupA does not have.
5. Add the missing permission node to GroupA.
6. Return to step 1 (above) and test the /fly command again.
--------------------------------------------------• If, after following all of the above information, you still have a problem with PEX on your server, post a thread in this official PEX forums and I will help you out as soon as possible. I handle all of the permissions.yml and command related issues on these forums, and I check the forums a couple times a day (at least).
When posting in the forums, always include your permissions.yml file (at the very least) and include your server console log from the time the server starts until the server has finished loading. These 2 files can be linked from Pastebin or attached to the post you make in these forums.
DO NOT EDIT THE FILES BEFORE POSTING OR ATTACHING THEM. Removing the users section and other information will make helping you out much, much harder (in many cases).
I almost never notice I have private messages, and it's actually considered rude to PM authors here. Definitely do not message the entire staff of a plugin, especially not all in one message.
--------------------------------------------------• If you have SQL or programming related problems and questions, you must send in a ticket. I do not handle any of those issues on these forums; only Zml (the actual PEX programmer) handles those problems.
--------------------------------------------------I will add more to this list as I remember stuff.
Official PermissionsEx Guru* (*not the PEX programmer)

Basic PEX Guide | Prefix/Suffix Guide | Troubleshooting Guide
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