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Hi, the plugin ignores both the flow of the document and the Articles panel layout and orders the elements in the output based on the document XML structure (the order they were created in?). This produces HTML that is not readable by screenreaders such as Apple's Voice Over (the text isn't read in correct order). I guess the easiest way to fix this would be to support the Articles panel content ordering.
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Yes, the document is structured for layout.

So if you want it to read in order, put the first items in the back of the stacking order in InDesign, and the items you want read last on top.

More on accessibility:

by (197k points)
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However, that really isn't how accesibility is done. This way you have no way of checking the order of things. Moreover ID has features to handle this, the plugin should support them. One of the main reasons to go with html instead of pictures (as for example most ipad mags still do) is to make the content accesible to everybody.
The features in InDesign (Articles/XML structure) are designed for a different type of content, and don't necessary respect page breaks or layout.

It might be possible to re-order the structure, but it would mean adding a lot of complexity to the HTML/CSS in terms of z-indexes.

A simpler solution might be to include a script that changes the stacking in InDesign (before export) to match the intended read order.
That is what Articles panel is for – can't you use the ordering provided there? ID uses it in PDF export may be the behaviour can be copied somehow? Or would it cause much trouble to order objects by their coordinates on a page (reading left to right, top to bottom)?
I can look into it...BUT...articles can span multiple pages, so it doesn't blend well with paginated output. If you want article-based output, the EPUB export does a nice job. It's just a different approach. in5 is designed around layout.