Chris Green wrote:

> When diving into more documentation, I was very confused because the
> textclass of the paragraph following the Section header was also
> called standard yet it was not indented so I looked around and found
> the NoNextIndent 1 in all the Section style definitions.  Removing
> them allowed the first paragraph to be indented and look like the rest
> of the text.

the lyx paragraph-layouts, like enumerate, standard, section, a.s.o.
don't correspond to the latex-layout in every way. the lyx layout
is part of the wysiwym. for example: when you choose the helvetica
font and a document fontsize of 12pt, nothing happens in the lyx 
layout, you always see the same or What You Mean. 

> \usepackage{indentfirst} does what I need in the cleanest way.  My
> kludge of getting rid of 'NoIndentFirst 1' does it both ways but I'm
> sure is subtlety  breaking things that I do not yet understand.

it's a typographical standard that you don't indent the first
paragraph behind chapter/section/.../lists like enumerate/..

with package indentfirst you change your latex-layout, not
the lyx layout, which always corresponds to ~/.lyx/layouts/...

> I'm confused though at what type of things go in a layout and what
> type of things require a LaTeX package.

important is not the fact what you see on screen but what you mean.
it's a kind of a compromise between users and developers: all must
be easy, for both! 

> Layouts, as I understand them
> are ways to relate the different portions of a document together and
> how they should act in relation to other sections.

that's right, but there are a lot of latex packages available,
no one knows how many ..., therefore you can't get a wysiwym
for lyx (lyx-layout corresponds to latex layout), it makes 
absolutely no sense!

> LaTeX packages of various sorts can perform any of these actions so
> I'm confused as to when one should think in terms of Layout
> abstractions and when one should dig lower. Is there a general rule?

for example: if you use a latex package very often, which corresponds
to no lyx layout, than it makes sense to extends your lyx-layout. 
have a look at
http://www.educat.hu-berlin.de/~voss/lyx/layouts/layout.phtml
if you ever want to indent your first line, you should change the
lyx layouts for chapter/section/... and load the package indentfirst
by default. write in (for example) stdclass.layout

Preamble
  \usepackage{indentfirst}
EndPreamble

and change the other layouts just you've done. 

Herbert

-- 
http://www.educat.hu-berlin.de/~voss/lyx/

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