ScriptFinder: discover each script only once

Even if overlapping base script directories are added, such that a
script might be examined more than once, let's only add it to the first
time it is matched.

This will be useful to support Fiji 1.x's special handling of scripts in
the Plugins/Scripts subtree.
ScriptFinderTest: add test for overlapping dirs
ScriptFinderTest: avoid emitting warnings

The default scripts directory is not actually present, so let's exclude
it from our search. This avoids warnings about nonexistent scripts
directories.