@jasonekratz I like your idea.
I have used a local copy of JavaScript and CSS files that I linked into markdown. It is not my preferred solution.
Providing a way for users to add their JavaScript and CSS files to the Application Support folder would be better because it would not require us to alter existing and new documents with links to custom files. Some of us have many existing markdown files and hope to have many more.
The ideal solution would be to have a file in the Application Support folder that is always included when a markdown file is rendered by DEVONthink. The file could be empty by default and thus would not alter behavior unless action was taken by the user. A user could include links in that file to their own prism.js and prism.css. Those custom prism files could reside in this same location in Application Support as the include file. This would permit the customizations to persist over upgrades (much like they would if they were stored in a DEVONthink database). It would also permit us to share the markdown rendering across many DEVONthink databases since the files are equally available to all the open DEVONthink databases. This would also allow users to include other files beyond prism. Who knows what kind of amazing customizations users could include in their markdown files?
The key for me, for this include file suggestion, is being able to change the rendering of my markdown files without having to alter the sources.