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Does one generally incorporate the APIs themselves into a developer's guide?
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I wouldn't. I'd keep it online mostly because you WOULD end up with a very large document and honestly it's easier to find something if it's online than in a printed manual. (my opinion at least) Plus, it would be nice to be able to have both the developer's guide and the API open at the same time, making it possible to jump into the API without losing your place in the developer's guide. This opinion is mostly based on my own limited experience. Whenever I've needed to find out something from an API doc, I just wanted to get in, get the info I needed, and get out. Thumbing through pages and pages of stuff to find what I want was annoying. :-) but that's just me.
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If it is not usual to incorporate the APIs in the developer guide, what DO you put in a developer guide? Do you refer the reader to the (separate) APIs? How would you refer them to a Doxygen suite of HTML pages?
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"Well, now, that's the trick, isn't it." :-) I'd think that if you are mentioning the API, you're probably mentioning a specific method, property, etc. You should be able to get away with, "department.documentation.writer.toil() creates your documentation with a little magic and a lot of sweat (see the API for more info)" or something like that. It would be easy enough to navigate into the API to find that particular item.
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