This comes from MDL-4143.

Since ages ago we have been using $module in mod version.php files. And $plugin is the used by all the rest of plugins (also supported by mods).

So this is about to:

1) Deprecate the $module uses for 2.6 (long life, to be erased in 3.0). Debug bad uses.
2) Change all core occurrences to $plugin for 2.6.
3) Documentation and modtemplate too.

Ciao