Scientific Review Book

Any decent word processor can build an index. Some claim to do it automatically. The problem with software index generation is that it doesn't know whether it is important to index a word and will index all instances, building a concordance instead of an index.

It's not an arcane art: as the author, you should know which is the important text and which is the minor mentions. I print a copy of the manual and and manually highlight all places where a word should be indexed: normally where the text explains its function, and how to install, use and fix whatever. Then I go through the file inserting index marks with the word processing or page layout software. Some important concepts are multi-entry spots, indexed by the noun and the verb the user is likely to be looking for: Mouse installation and Installing the mouse.

Be consistent with yourself and industry standards: one large page layout program used "expunge" where everyone else used "delete" among their many vocabulary quirks ... it was annoying beyond belief because the typical choices were not even given a Delete (see expunge) entry.

The sidebar comments would be a form of cross reference field - one set up to show page numbers - probably in a floating frame. Again, it's easiest to make a manual markup with hand-written notes and then insert the codes in the frames.