To clarify, David, when you say "it just worked" you mean that when you select 
Edit > Indent > Indent lines then the line containing the insertion point is 
moved (left or right, as appropriate) to conform to standard Lisp indentation 
conventions with respect to the code above it (e.g. with respect to the 
position that you are within an s-expression, etc.)? 

I note that there is some variation in what is the "standard" Lisp indentation 
convention in some cases, e.g. in certain special forms as opposed to ordinary 
s-expressions, but mainly I want to know what it is that you do to make "it" 
work and roughly what "it" is that then happens. I've had similar conversations 
with people in the Bluefish community and it turned out that for at least one 
person "auto-indenting" just meant lining up with the first non-blank line of 
the preceding line, without regard to the Lisp syntax. I kept saying that "it" 
wasn't working but it turned out that "it" was -- it's just that "it" wasn't 
what I meant by Clojure-aware auto-indenting.

Assuming that I understand what you mean by auto-indenting, and that you invoke 
it with Edit > Indent > Indent lines, does this also work for you for all lines 
of a highlighted selection? 

In other words, I'm not yet sure if I'm actually experiencing a problem or if 
I'm just looking for a feature that isn't there. It would help me to know a 
little more about what you do and what you see when "it just works," so that 
I'll have a better idea of what I should ask/tell the maintainer.

Thanks,

 -Lee

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