Workflow can be -
1. Initially, user creates some top-level categories manually. Ex. programming languages, philosophy, art, computer networks, etc.
2. Tool starts filing bookmarks under these top level categories and further creates sub-categories by itself where it's obvious (e.g. under prog lang - python, js, java, etc)
3. Only if the tool is unable to find categories clearly, it should require user's attention.
For #2, tool should use factors like content, tags used by author in article, what type of content website usually posts, etc and generate score. If multiple categories above 90% score, bookmark under all those categories.