OK, here's a clue re: the first issue.

The flymake "nodes" ( https://www.gnu.org/software/emacs/manual/html_node/flymake/ ) manual (attempts) to make a relative "cross link" to the eglot "nodes" manual, like so:

<a data-manual="eglot" href="../eglot_html/Eglot-Features.html#Eglot-Features">Eglot Features</a>

That "relative cross link" must not work, apparently, within the server tree at /software/emacs/manual/

This happens regardless of https://www.gnu.org/software/emacs/manual/html_node/flymake/ vs. https://www.gnu.org/software/emacs/manual/html_node/flymake/index.html

(I was hasty+wrong in claiming that that distinction was pertinent.)

OTOH, FWIW, the *mono* manual https://www.gnu.org/software/emacs/manual/html_mono/flymake.html links like this

<a data-manual="eglot" href="eglot.html#Eglot-Features">Eglot Features</a>

... which works.

On Thu, Aug 22, 2024 at 2:24 PM Eli Zaretskii <eliz@gnu.org> wrote:

> From: Lester Longley <lester@ieee.org>
> Date: Thu, 22 Aug 2024 14:21:25 -0400
> Cc: 72761@debbugs.gnu.org
>
> Thanks for taking a look at these items.
>
> Re: the first issue, on further experimentation,
> it actually seems to manifest itself (as
> https://www.gnu.org/software/emacs/manual/html_node/eglot_html/Eglot-Features.html#Eglot-Features)
> only if I go to this URL (w/o the trailing "index.html"):
> https://www.gnu.org/software/emacs/manual/html_node/flymake/
> ... which must be the way I originally stumbled on this.

Then I guess someone who knows more than I do about HTML will need to
explain what happens there...