Some plugins are not being initialized correctly due to the way plugins in workunit are generated

Thor (and other engines?) depend on the <Plugins> section of the workunit, to initialize the plugins (call setPluginContext or setPluginContextEx).

But it seems (depending on client?), the <Plugins> section is being generated differently, sometimes the plugins have the so extension, other times they do not.
They will only be initialized when they do.

Many plugins will continue to function without the context initialization, but if they are initialized by 1 query, then not re-initialized by a subsequent one, the latter will be using a stale context and crash.

Also, at least 1 (address cleaner) depends on this initialization to function correctly.