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).
Eclipse itself is using the PDE build infrastructure that it ships with the Plug-in Develeopment Environment. Ant is used to run the build, with adequate plug-points where in you can perform custom tasks such as instrumentation of code.
To get comfortable with ant:-
http://ant.apache.org/manual - If you are new to ant
Eclipse provides a very usable interface for writing ant files(yes, with auto-complete and the stuff) as well as run the ant files from within the IDE. But, for headless(without UI, from command line) builds, you'll need to use the antRunner application provided by eclipse. For more help, peek into the help documentation of eclipse that you are using.
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."