Setting namespace prevents plugin writeFile calls

[jrburke]

Originally reported on requirejs list.

Basically, pluginCollector is passed in pragma.process() in the 'OnSave' pass, after the namespace changes have been done, so the parse.findDependencies in pragma.process() fails, since findDependencies is not namespace-aware.

The solution may be allowing findDependencies to be aware of namespaces. This means changing a bit more of that AST pass.