RDF files were not stored in the VIVO home directory
The build.properties and runtime.properties files were a single file, called deploy.properties in the VIVO installation directory.
Step-by-step guide
Things to think about
If you've made changes to code, e.g. changes to freemarker template files, etc... then you might want to consider branching the VIVO and Vitro github repositories. This would act as a "backup" of any changes that you've made and backups would be handled by, say, github. There is a vivo project template on Github that is an example of this approach. It uses Git submodules to track the VIVO and Vitro code and keeps local modifications in the local git repository. A VIVO site could clone this repository and have a blank instance to get started with and have the benefit of any local changes being in a git repository. The Brown VIVO modifications are a working example of this approach.