Hi, thank you for the review.

> I'm not convinced that inserting label and, more importantly,
> caption within the environment is the way to go. For example, that
> will not work when `org-html-with-latex' is set `verbatim'. Couldn't
> we simply wrap a HTML label and caption above, or below, the whole
> environment so it DTRT in all cases?

It is true that my patch did not address the verbatim mode, I was
focusing on the MathJax output.  The reason I initially decided to rely
on MathJax is that I thought it would be better to take advantage of
MathJax support for LaTeX label and references.  It was then sufficient
to delegate rendering of the latex-environment and links to ox-latex,
although I ended with some unpleasant code to achieve that.

To make sure I understand the desired HTML output, do you mean that
instead of producing this HTML:
,----
| \begin{align}
| \label{eq:orgbfedefe}
| 1 + 1 = 0
| \end{align}
`----
and relying on MathJax to manage references, we should produce something
like the following?
,----
| <div id="orgbfedefe" class="equation-container">
| \begin{align}
| 1 + 1 = 0
| \end{align}
| <!-- insert the equation number -->
| </div>
`----

Am I understanding correctly?

The advantage of this approach is that it is consistent with how the
other types of references (figures, source blocks, etc.) are managed and
it should work with the verbatim mode.

I have a few questions about the "caption" (i.e. the equation number):

1. Where should it be placed?  In a `<span>' tag like it is done for
   figures?  Ideally, I would like to have the caption (i.e. the
   equation number) on the right side of the equation, as it is done in
   LaTeX, should this be done with CSS?  Should there be a user option
   for the position of the caption?
2. Should we disable MathJax's equation numbering and replace it with
   ours?  I am afraid this may break the setup of users already relying
   on MathJax to label and reference equations.
3. Should there be an option to customize the formatting of the equation
   number, both on the right of the equation itself and in links
   (e.g. wrap the number between parentheses, as `\eqref' dose)?

The attached patch tries to implement some version of this approach.
The code looks less hackish to me, but I still rely on a variable
external to ox-html.el: I use `org-latex-math-environments-re' to
determine if the LaTeX block is a math block; this is used to limit
counters to equations environments, ignoring other types of latex
environments.  Also note that I did not disable MathJax auto-numbering
in the attached patch, so equations have two numbers.

My main concern with this revised version of the patch is the possible
conflicts between MathJax and org equation numbers:
- Only one equation number should be shown, and MathJax and org counters
  may not match (e.g. with multiline equations).
- If we disable MathJax auto-numbering, it seems that we would be losing
  the possibility to have labels on individual lines of multiline
  equations.  Is it true?

Please let me know how you would like me to move forward with this.

Thanks in advance.

thibault