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I have been using pdfunite utility for joining multiple PDF files without much hassle, however, I have observed that bookmarks of the first file are retained but of the rest are just lost; such isn't observed while I use Acrobat 8pro (under wine). Plus the added benefit of the latter is say that I have two files:

1] Introduction.pdf

2] Result.pdf

then when I join these files the resulting file will have two bookmarks corresponding to parent files' names. Is this functionality provided by any linux native utility or some bash...

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Yes, this is possible with sejda:

  1. Download and install the latest sejda-console debfile
  2. Use the following commandline to merge your documents:

    sejda-console merge -b  one_entry_each_doc -f file1.pdf file2.pdf -o merge.pdf
    

    where file1.pdf and file2.pdf are the paths to your PDF files and merge.pdf the path to save the resulting PDF to. You can include as many PDF documents as you want.

    -b one_entry_each_doc will discard of all existing bookmarks and replace them by one entry for each document. If you want to preserve all bookmarks for all documents you will have to use the -b retain option.

    I am afraid there is no way to both retain all bookmarks and add a new entry for each document, at the moment. Though there is a feature request regarding this very functionality.

For a full listing of all sejda merge options check out my answer over at superuser.com.

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