I advise candidates to annotate their thesis, but the word really in my mind is augment:
To make something greater by adding to it…
You’re not just adding some notes or bookmarks, some Post-its or highlighted sections; your thesis will be better for you doing it.
I use the word annotate in workshops, because that’s what people expect. Let’s be clear though: if you add Post-its to show the start of chapters, underline typos, add notes in a consistent way, highlight references, insert clarifications, decrypt technical language, update a thought and anything else like this – you’re augmenting. Your thesis is greater than it was, a richer resource for you.
Step one, ask yourself: what would make your thesis even greater for you?