When you install JBT nightly from http://download.jboss.org/jbosstools/updates/nightly/core/master/ into Eclipse and during the build, a new nightly build replaces the old one, you can get a failure like this:

http://download.jboss.org/jbosstools/updates/nightly/core/master/features/org.jboss.tools.wtp.runtimes.tomcat.feature_1.1.0.Beta3-v20140603-0027-B526.jar cannot be found

This is because during your install, the old jars were replaced with the new jars, i.e. different filenames.

I'm not sure if it's something we really need to fix, it's open for discussion. But it happened to me yesterday and it wasn't the first time, so I'm throwing it on the table.

Nick offered this alternative:
install from a specific build folder instead of the "latest nightly"
http://download.jboss.org/jbosstools/builds/nightly/core/master/2014-06-04_06-40-59-B8878/all/repo/
http://download.jboss.org/jbosstools/builds/nightly/core/master/2014-06-04_09-46-40-B8879/all/repo/

But obviously that's just a workaround, not a real solution.
One way this could be achieved is this: plugins/ and features/ would contain jars from both the latest and previous builds. This way if you start installing (latest=build N) and in the middle of your installation there is a new build (N+1), there would still be jars for both N and N+1 builds.