This page is about building Eclipse- and RCP-based products (including Eclipse itself).
PDEB is The Way to headlessly build Eclipse- and RCP-based products. The best currently available guide to PDEB is still Markus Barchfeld's Build and Test Automation for plug-ins and features, though it's getting a bit old (having been written for eclipse-3.0).
Plugins (including features and fragments) must specify their own versions as well as the versions of their dependencies appropriately.
See the eclipse team's plugin-versioning guidelines. You can also ask Pascal Rapicault or John Arthorne for their "Plug-in versioning" presentation.
Pascal Rapicault has created an application (org.eclipse.core.runtime.versionchecker.dependencyChecker) to "specify the ranges on all [your] required plug-ins."