Some other findings:
-If your App_Data/ClientDependency directory grows too large. You can safely delete it and it will be regenerated.
-There currently is no mechanism in DNN to automatically clean up the App_Data/ClientDependency directory. I've created a ticket for this: http://support.dotnetnuke.com/issue/V...
-Hitting CTRL-F5 in your browser window is supposed to completely clear your cache and allow you to view the latest changes without having to do any type of "Clear Cache" or reset on the server side. But, I couldn't get this to work in Firefox or Chrome. If I browsed to the site in a new browser or incognito mode, I did see the changes.

I hope to compile all the information I gather an update the appropriate wiki entries with it once I know what's true or not so other people don't have to go on the journey of discovery I've been following. Of course, if someone else wants to do this, I won't be upset.

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David O'Leary
Efficion Consulting

If you remove the clientDependency section from the web.config entirely, it seems it will cause none of the CDF managed files to be included at all. I was able to trim the clientDependency section in the web.config down to the following without affecting functionality

  <clientDependency fileDependencyExtensions=".js,.css" loggerType="">
    <fileRegistration defaultProvider="LoaderControlProvider">
      <providers>
        <add name="DnnPageHeaderProvider" type="DotNetNuke.Web.Client.Providers.DnnPageHeaderProvider, DotNetNuke.Web.Client" enableCompositeFiles="true" />
        <add name="DnnBodyProvider" type="DotNetNuke.Web.Client.Providers.DnnBodyProvider, DotNetNuke.Web.Client" enableCompositeFiles="true" />
        <add name="DnnFormBottomProvider" type="DotNetNuke.Web.Client.Providers.DnnFormBottomProvider, DotNetNuke.Web.Client" enableCompositeFiles="true" />
        <add name="PageHeaderProvider" type="ClientDependency.Core.FileRegistration.Providers.PageHeaderProvider, ClientDependency.Core" enableCompositeFiles="true" />
        <add name="LazyLoadProvider" type="ClientDependency.Core.FileRegistration.Providers.LazyLoadProvider, ClientDependency.Core" enableCompositeFiles="true" />
        <add name="LoaderControlProvider" type="ClientDependency.Core.FileRegistration.Providers.LoaderControlProvider, ClientDependency.Core" enableCompositeFiles="true" />
      </providers>
    </fileRegistration>
  </clientDependency>

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David O'Leary
Efficion Consulting