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https://issues.apache.org/jira/browse/FOP-2520?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14713551#comment-14713551
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Björn Kautler commented on FOP-2520:
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Ah, thanks for your help guys.
Actually it is the preprocessing of the file.
The profiling step we do before the DocBook->FOP for making the Doku customer- 
and build-specific actually inserts newlines between the <indexterm>s, so the 
input DocBook for the DocBook XSL is

{noformat}
         <para>
            <indexterm significance="normal">
               <primary>table</primary>
               <secondary>customize columns</secondary>
            </indexterm>
            <indexterm significance="normal">
               <primary>customize</primary>
               <secondary>table</secondary>
            </indexterm>
            <indexterm significance="normal">
               <primary>filter</primary>
               <secondary>table</secondary>
            </indexterm>
            <indexterm significance="normal">
               <primary>table</primary>
               <secondary>filter</secondary>
            </indexterm>You can customize most tables in the product. The 
configured table view is saved in your user profile and will be restored when 
you start the prouct the next time.</para>
{noformat}

I'll try to find out whether I can prevent this.
But still I wonder why it does not work even with that input and why it works 
fine with XEP.

> Empty elements consume space
> ----------------------------
>
>                 Key: FOP-2520
>                 URL: https://issues.apache.org/jira/browse/FOP-2520
>             Project: FOP
>          Issue Type: Bug
>    Affects Versions: 2.0
>            Reporter: Björn Kautler
>         Attachments: empty space that should not be there.png
>
>
> If you use {{indexterm}} tags in DocBook, the DocBook XSL stylesheets 
> generate empty {{fo:wrapper}} or {{fo:block}} elements with an {{id}} 
> attribute. These elements take up visible space if processed with FOP. Using 
> XEP, those empty tags do not consume any space.
> Here an example excerpt from a FO file in question and [attached|^empty space 
> that should not be there.png] the result.
> {code:xml}
> <fo:block space-before.optimum="0.6em" space-before.minimum="0.4em" 
> space-before.maximum="0.8em">
>    <fo:wrapper id="N1004F"><!--table, customize columns--></fo:wrapper>
>    <fo:wrapper id="N10056"><!--customize, table--></fo:wrapper>
>    <fo:wrapper id="N1005D"><!--filter, table--></fo:wrapper>
>    <fo:wrapper id="N10064"><!--table, filter--></fo:wrapper>You can customize 
> most tables in the product. The configured table view is saved in your user 
> profile and will be restored when you start the prouct the next time.
> </fo:block>
> {code}



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