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I agree with the other responses. PDF was the original iLiad target format, and is still the only format with markup capability.
HTML support is marginal. For single-file HTML, FBReader is best. Otherwise I would convert to the MOBI format, but that would still not allow you to comment on the text.
In fact, the Kindle may be better suited to your needs. You would again have to convert to MOBI, but then bookmarks and comments can be made via the keyboard. Comments are saved in separate text files, but these are fully searchable.
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