We’ve published a web page on Using Hook with Bookends Reference Manager by Sonny Software – Hook. This includes an alternative integration script , for users (like myself) who would rather traffic in hook://file/ URLs than in bookends:// URLs.
More generally, when an app (like Bookends) has its own URL scheme (like bookends://), that is what we tend to build into Hook’s integration with the app. However, if (like Bookends) it’s a file-based app, we may in addition publish an alternative script that returns hook://file/ URLs. However, sometimes we find even if the app has its own scheme it’s better to make hook://file/ the default scheme. But in that case we also publish a script that uses the app’s native URL scheme.
Some of the pros and cons of the different URLs schemes with respect to Bookends are briefly listed on that page.