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The main difference in these files is the presence of nihvivo.dir.  This attribute points to where VIVO is for the build.  There are two standard ways to setup VIVO, for development or deployment.

Development

With development, you want to look at your VIVO against the VIVO and Vitro sources. This means getting the source for each project from the git repository.

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Your deploy.properties then points at the individual repositories.  When you build it pulls the three repositories together and sends them as a single package to Tomcat.

Deployment

In deployment you have just your third tier and the released source for VIVO. In that released source is the vitro code that goes with the latest release of VIVO. Your deploy.properties for a deployment build will need to point to the internal vitro-core folder for the vitro code.

Project template

If you would like to get started with the three tired build process, there is a project template on Github that includes the necessary build.xml, build.properties and directory structure.  This template uses Git submodules to pull in VIVO and Vitro from the main vivo-project repository.  

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