NEXUS-5661: Proxy repo prefix file does not include paths only available from local storage

Code change and UT (by reusing PrefixFileForProxiesAreUnmodifiedTest)
that would test an untrue condition. This change implies that
proxy prefix files are not unmodified anymore.
NEXUS-5661: Fixing the UT

Now that the local storage is counted as prefixes source,
the nuking of local storage happened at bad place, after
prefix file was rebuilt.

Moved local storage nuking to proper place, to
happen before prefix file is rebuilt.
Merge pull request #31 from sonatype/nexus-5661-prefix-file-merge

NEXUS-5661: Proxy repo prefix file does not include paths only available...