I'll confine my comments mainly to the content of the document. There are also problems with the layout and use of images which I won't delve in to too much. As English is not your first language (I assume) we'll make allowances for that and I'm sure that others will help you in that respect.
The term "jump labels" is not one I've heard of before. Perhaps that needs a bit more explanation.
For this part of the document:
* Explain what each of the com_* and mod_* folders represent, and within each of those folders what each subfolder represents. Also, list each file and what can be found in the file.
o com_contact - Contact Component
# default.php - Contact Category Listing Headings and Footers
# default_items.php - Individual entry for each Contact in a certain category
# default.php - Basic Contact Information for an Individual
# default_address.php - Contact Address, Phone, Fax, Mobile, etc. Information
# default_form.php - Form that shows Basic Contact and Address information for a specific person
I don't think the images you are including really add anything other than visual clutter. I suggest you drop them and just use the outlining facility in OO.
I think you have too many examples which are somewhat repetitive. I would think just 2 or 3 examples (at most) would suffice. As a rule, if an example doesn't add anything new that hasn't been shown before, then don't include it.
I can see the difference in the HTML generated (going from tables to divs), but in most examples I am struggling to see any visible difference in the rendered output. If there is no difference then you don't need to show comparison images; if there is a difference I think you will need to point it out a bit more clearly.
In some examples, the output seems to go from having multiple columns to just a single column. Is that the intended change? I'm wondering why anyone would want to do that as it seems to be reducing readability. If the only change that the overrides are achieving is to go from tables to divs then perhaps small changes in the rendered output are largely irrelevant and there is little point in focussing the readers attention on those differences. Maybe just a single image would suffice to show the reader what part of a typical Joomla! website is being affected.
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