That is a good question! To my knowledge, there is no way to directly control DEVONthink’s indexing mechanism and get it to ignore certain file types. However, one can resort to using a smart folder. Here’s how I do it, as an example to get you started.
I have a top-level folder in my database called Sources. Within that, I have a folder called Zotero and within that, I put the actual indexed folder. (The reason for this indirection is purely aesthetic: I index the storage folder inside my Zotero database folder, since that’s where Zotero stores PDFs, but I find the name storage confusing in the context of the rest of my folder structure in DEVONthink. The indexed folder cannot be renamed in DEVONthink because it matches whatever’s on disk, so the only option left is to create another folder in DEVONthink and call that one whatever I want.)
WIthin the folder Sources, I put a smart folder that searches inside the storage folder. Here’s its definition:
I’m not convinced this particular smart folder definition is ideal; for one thing, if I ever put another file type into my Zotero database, I have to remember to update the smart folder definition to include it. But it’s good enough for now, and it avoids all those css, js, and other files that may end up in a Zotero folder. It produces a very clean list of articles:
Hope this helps!