1. If your property/method doesn't appear after running doc generation,
that means you need to specify @memberOf in object literal

But if you are using prototype, you don't need to do this; jsdoc would know the relationship.

2. {@private|@access private} marked section would not appear in the document unless you do specify -p when running jsdoc.

3. If your google closure linter is not happy when you do |git commit|, add a tag here:
https://github.com/mozilla-b2g/gaia/blob/master/Makefile#L878

4. Use conf.json to release you from typing a long command to generate the docs. Mine: https://gist.github.com/alivedise/7904430

5. Since jsdoc supports markdown, there's nothing could prevent us from having an architecture diagram image in the doc instead of drawing with ASCII characters.
Sample: http://alivedise.github.io/gaia-system-jsdoc/module-AppWindowManager.html#init
(I'm using http://cacoo.com but open to know if there's any better solution for making diagrams/flowcharts.)