If you’re looking for more information on what’s called warehouse aka remote resources, @willwood has a free book he posted a couple years ago. Although a couple years old everything still applies.
RapidWeaver’s resources used to be very unreliable, so the whole concept of using direct URL’s to link to images(somehow got the name warehoused) became popular.
Part of RapidWeaver 8 was a total rewrite of the recourse management process. I’ve found it to be very stable as long as you ensure the option in the advanced settings are set to make document portable(prior to 8.1) or
Site Resources: Copy into Document (8.1 beta).
Something to keep in mind about “warehoused” resources, you’re using an absolute URL to every resource. If you change the URL (eg. add SSL) you’ll need to change the link addresses for every resource, every single place it’s referenced.
The real culprit in your case was Clean My Mac. Most all of these cleaning utilities cause all kinds of problems and should never be installed.