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When creating a new project for a client, we will use the following folder structure in the repository:

The plugins and projects folders are where the client specific code will reside. If, for example, the client doesn't have a custom plugin for their application then that folder will be empty.
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The following image is an example of what one would find in the workspaces/application area of the project repository. Note that it is just a container to link every part of the client application. It even points back to the projects folder within the same account folder.
The externals can also contain revision numbers for specific code bases (eg. plugins, core framework, etc). When deploying it is highly recommended you add the revision or specific tagged release for plugins/frameworks you are not actively developing to maintain a stable distribution. An example of revision number use is as follows:
Apache Setup
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