Thanks for that, Wolfgang. I can only hope that, as the culprit is known, it 
can be apprehended!

Idris: here is the document that I had sent (and many thanks to you and to 
Pablo for the more general advice):

>  \unexpanded\def\doVariant#1#2#3%
>       {\startlinenote[#1]{#2] #3}#2\stoplinenote[#1]}
> 
>    \newcounter\countvariants
>    \unexpanded\def\variant
>       {\doglobal\increment\countvariants
>        \normalexpanded{\doVariant{Varia:\countvariants}}}
> 
> \setupalign[r2l]
> 
> \showframe \starttext 
> 
> \section{Correct}
> Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque 
> molestie dictum quam non congue. Integer ut dolor vel mi vestibulum molestie 
> vel et nulla. Morbi id justo vitae quam rhoncus tincidunt ut adipiscing nisi.
> 
> \section{Incorrect}
> \startlinenumbering
> Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque 
> molestie dictum quam non congue. Integer ut dolor vel mi vestibulum molestie 
> vel et nulla. Morbi id justo vitae quam rhoncus tincidunt ut adipiscing nisi.
> \stoplinenumbering
> 
> \stoptext

All the best,
Talal

> On 1 Aug 2015, at 19:47, Wolfgang Schuster <schuster.wolfg...@gmail.com> 
> wrote:
> 
>> tala...@fastmail.fm <mailto:tala...@fastmail.fm>     1. August 2015 17:37
>> Sorry to pester, but this problem is barring me from moving my book project 
>> into ConTeXt this weekend.
>> 
>> The use of linenumbers seems to throw off the R2L mechanism. Example of the 
>> problem attached. 
>> 
> 
> The culprit is the function "boxed.stage_two" in page.lua which output each 
> text line in the line numbering
> environment in left to right mode. When you have justified lines everything 
> is fine but when you have a ragged
> line (e.g. the last line in a paragraph) ConTeXt aligns the context with the 
> left margin.
> 
> \starttext \showframe
> 
> \startalignment[righttoleft,flushleft]
> 
>     \input ward
> 
>     \blank
> 
>     \startlinenumbering
>     \input ward
>     \stoplinenumbering
> 
> \stopalignment
> 
> \stoptext
> 
> Wolfgang
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