The documentation is awfully incomplete. For instance the main referenced page, https://github.com/PEXPlugins/PermissionsEx/blob/master/doc/Tutorial.md, has links at the bottom for further reading, that go nowhere.

No to mention the content is just wrong. IE, "On first launch, configurations will be created in the config/ninja.leaping.permissionsex folder for Sponge, and plugins/PermissionsEx for Bukkit. 1.x", which is 100% inaccurate.

When directing people to this documentation, it would be nice if it were actually complete and accurate.

As PEX 2.x has not been officially released yet— it's still in development —the documentation is also not fully released yet.