Check which is the newest wrapper for multiple wrappers

Thanks to @tuncK we found that there are tools that have been migrated (e.g. to IUC), example: https://github.com/bgruening/galaxytools/tree/master/tools/mcl
So they exist in multiple locations.
I think the tool_extractor overwrites an entry if the names are identical, so we would need two things:
a) allow storing multiple entries for tools with identical `Galaxy wrapper id` (maybe we should rename that to shed id as well ?)
b) a way to filter for the newer wrapper, maybe based on the one with the latest commit.

Start by examining the tool_extractor behavior described in the issue and compare the example migrated and existing wrapper locations. Determine how duplicate Galaxy wrapper IDs should be stored and how the latest commit should identify the newer wrapper; done means both entries can be retained and the newer one can be selected.

Written by the indexing model from the issue text.