The Ink theme template files have now disappeared when I click on Edit Custom Themes. I see a thumbnail of the Ink theme at the top of the Design page, but no access to its related files.
Plug-in-based themes, like the Ink theme, is still a work in progress. I know @manton is working on changes related to this today. So I’m sure you will be able to reaccess template files again, sooner or later. 
Yep, this is part of a series of changes we’re making to improve plug-ins. The problem with directly editing plug-in templates is that they get overridden when there’s a new version. Instead of editing the plug-in templates directly, create a new custom theme and edit that. If Ink is set as your theme, you’ll see the Ink templates there too and can change them.
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One thing I should clarify: if you are the creator of a plug-in, those will still show up under Edit Custom Themes, but in a new section at the very bottom of that page.
Or can you just add in support for @sod’s two plugins (Reply via Email and Conversation on Micro.blog) in the Ink theme? 
I hate to create a custom theme just for this?
Thank you for this update. I had noticed the pattern of update plugin → overridden edit. I have just created a custom theme for Ink and made the necessary edits. // @sod
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