[JimmXinu]

Originally Posted by ericpaul

Thanks for this plugin. I'm merging some music notation files from Finale, which I've output from Finale as epubs. They merge fine, but the pages of music in the resulting file display much smaller when I view them in the iBooks reader, compared to the size they were displaying in the original epub files (as if the margins have changed, or extra white space has been added all around the music notation).
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Originally Posted by ericpaul

Here are the attachments (they were removed temporarily while the moderator verified that I was the actual copyright holder, which I am).
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Your original epub (from Finale) use some EPUB 3.0 features related to fixed layout and (I think) some iBooks specific extensions.

Unfortunately, EpubMerge outputs EPUB 2.0. The fixed layout settings and 'prefix' extensions aren't carried over. And EPUB 3.0 metadata layout has changed enough that it's not a simple matter to copy those settings over.

(There's been discussion again just in the last couple days about why Calibre in general doesn't support with EPUB 3.X. I don't plan to support EPUB 3 until Calibre does.)

Some details of the content.opf:

Spoiler:

Highlighted in red are parts that, if removed, cause the larger margins to appear in iBooks.

<?xml version="1.0"  encoding="UTF-8"?>
<package xmlns="http://www.idpf.org/2007/opf" version="3.0" unique-identifier="pub-id" prefix="rendition: http://www.idpf.org/vocab/rendition/# ibooks: http://vocabulary.itunes.apple.com/rdf/ibooks/vocabulary-extensions-1.0/">
  <metadata xmlns:dc="http://purl.org/dc/elements/1.1/">
    <dc:title xml:lang="en">Moment By Moment</dc:title>
    <dc:creator xmlns:ns0="http://www.idpf.org/2007/opf" ns0:role="aut" ns0:file-as="Elder, Eric">Eric Elder</dc:creator>
    <dc:identifier id="pub-id">/Users/eric/Music/sheetmusic/clearmymind/momentbymoment.epub</dc:identifier>
    <dc:rights>Copyright © 1999 Eric Elder.  </dc:rights>
    <dc:date>2016-05-16T05:00:00+00:00</dc:date>
    <dc:language>en</dc:language>
    <dc:identifier xmlns:ns1="http://www.idpf.org/2007/opf" ns1:scheme="calibre">893eef27-8265-4190-bd48-ec40a88d3bc8</dc:identifier>
    <meta property="dcterms:modified">2016-05-17T04:07:47Z</meta>
    <!--epub 3.0 fixed layout stuff:-->
    <meta property="rendition:layout">pre-paginated</meta>
    <meta property="rendition:orientation">auto</meta>
    <meta property="rendition:spread">landscape</meta>
    <meta name="calibre:title_sort" content="Moment By Moment"/>
    <meta name="calibre:author_link_map" content="{&quot;Eric Elder&quot;: &quot;&quot;}"/>
  </metadata>
  <manifest>
    <!-- Include EPUB 2 nav compatibility for Kobo 7.2.1 and other readers -->
    <item id="nav" href="toc.ncx" media-type="application/x-dtbncx+xml"/>
    <item id="toc" href="nav.xhtml" properties="nav" media-type="application/xhtml+xml"/>
    <item id="p001" href="p001.html" properties="svg" media-type="application/xhtml+xml"/>
    <item id="p002" href="p002.html" properties="svg" media-type="application/xhtml+xml"/>
    <item id="p003" href="p003.html" properties="svg" media-type="application/xhtml+xml"/>
    <item id="p004" href="p004.html" properties="svg" media-type="application/xhtml+xml"/>
  </manifest>
  <spine toc="nav">
    <itemref idref="p001"/>
    <itemref idref="p002"/>
    <itemref idref="p003"/>
    <itemref idref="p004"/>
  </spine>
  <!-- Include EPUB 2 guide compatibility for Kobo 7.2.1 and other readers -->
  <guide>
    <reference type="text" href="p001.html"/>
  </guide>
</package>

You might try seeing if Finale can output EPUB 2.0 instead of 3.0. Those might merge better.

Also, as the original copyright holder, I assume you're looking to create an omnibus ebook that you can distribute. EpubMerge is more meant for personal use. For example, EpubMerge output includes: <dc:rights>Copyrights as per source stories</dc:rights>. I won't tell you not to use it, but consider it an 'off-label' use.