It is a user setting, but you can change the defaults:
Email HTML formatting
Each JIRA user can specify in their own profile preferences whether to send outgoing emails in either text or HTML format. JIRA Administrators can specify a default email format by choosing the cog icon at top right of the screen, then System -> User Default Settings.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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