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ISIS-2062: updates to docs

  1. … 1172 more files in changeset.
ISIS-2062: flattens user guide

  1. … 89 more files in changeset.
ISIS-2062: updates to user guide

also adding in some missing anchors

  1. … 26 more files in changeset.
ISIS-2062: more user guide stuff

  1. … 10 more files in changeset.
ISIS-2062: updates docs on modules

  1. … 3 more files in changeset.
ISIS-2062: fleshes out module building blocks stuff

  1. … 3 more files in changeset.