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update wiki page
add proposed_taxonomy_api.md
pplacer and taxtastic already use phylo_model_file and not phylo_model as the file key in CONTENTS.json files, so making the spec match up.
Updated Reference package specification (rest)
Created Tree data structure notes (markdown)
add link to sphinx docs Updated Taxtastic wiki (rest)
Updated Taxtastic wiki (rest)
updated ref pkg spec
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update refpkg
tidy
deleted: algorithms.rst
merge
moving wiki files over from old repo
Initial Commit