I'm working on a project that has multiple theme/skin and is extensible via plugins.
As it stands right now my folder is structured as such.
vc/
  controller/
          home/
  view/
      classic/
           home/
      spring/
           home/
  plugin/
     feedReader/
             view/
             locale/
 template/
    header.html
    footer.html
Some things about this structure:
controller contains my controllers. 
view contains controller views; because the project uses multiple themes, views are segmented into a theme -- classic and spring -- folder.  plugin contains plugins with it's associated view and locale (language) data. template contains templates that may be included in my rendered view.
I'm using a template engine so with the output of each view I may include the template of a header and footer in addition to a left or right column containing one or more plugin. These templates may vary based on the theme, so there's a need to separate them based on theme.
My question is what might one recommend in terms of ideal folder structure. Right now things are spread across several directories, so import and export of views plus keeping track on files during editing can become tedious.