Fix dupes in deps provider, support atom pkgs

Whenever files were being locked *and* provided in rebar.config
duplicates could be printed. This is taken care of.

Also whenever atom packages were being used, they would cause the merge
step to fail. The new format does proper name-based deduplication of
resources, giving priority to locks to work.

ModificatioN/needs-update support is still in.

This may also act as a fix for #341, if automation isn't required too
much.

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