そんな時の対策（確認済）

$ gem uninstall theme
$ git clone https://github.com/Shopify/shopify_theme.git
$ sed -i -e 's/assets\//assets\/ sections\//g' shopify_theme/lib/shopify_theme/cli.rb
$ cd shopify_theme/
$ gem build shopify_theme.gemspec
$ gem install shopify_theme-0.0.25.gem

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ソース： https://github.com/Shopify/shopify_theme/issues/216#issuecomment-257918106

おまけ

開発は主にTim Anemaさんが担当しているようです。

linkedInの経歴に下記記載がありました。
• Go development of a command line tool for Shopify theme development https://shopify.github.io/themekit . I solely re-wrote the tool and built up proper documentation both for the command line and for using Themekit as an SDK