Dependencies that were previously obsolete are erroneously trimmed

[ctrueden]

When uploading files lib and dep to an update site, where lib depends on dep, and dep is currently an obsolete file (but would no longer be obsolete as a result of the desired upload), the dep dependency in lib gets erroneously pruned, since the Updater detects that dep is an obsolete file.

See also imagej/imagej-mesh-io#1.