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https://issues.apache.org/jira/browse/PDFBOX-3875?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16100241#comment-16100241
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Maruan Sahyoun commented on PDFBOX-3875:
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I created a set of testifies where I merged files with 

- only /Kids entries into one
- only /Names entries into one
- /Kids and /Names into one
- /Names and /Kids into one

and two times the same file (from a different directory) into one. 

The tool
- always generated only /Kids entries
- moves the /Outlines up one level
- adds the file name as the root of the previous /Outlines
- uses the same name for multiple occurrences of the same file name

PDFBox currently has issues with mixed definitions i.e. where a file with /Kids 
and /Names is merged. In addition merging the same file twice the entries of 
the second file point to the entries of the first. I'll have to investigate a 
little further if there are additional issues within the /Outlines entries(s) 
after merging.

> Bookmarks inactive after PDFMergerUtility
> -----------------------------------------
>
>                 Key: PDFBOX-3875
>                 URL: https://issues.apache.org/jira/browse/PDFBOX-3875
>             Project: PDFBox
>          Issue Type: Bug
>          Components: Utilities
>    Affects Versions: 1.8.9, 2.0.7
>            Reporter: Senthilvinayaham Murugan
>         Attachments: 000314.pdf, 000334.pdf, 000337.pdf, 001124.pdf, 
> 001929.pdf, 001995.pdf, Acrobat_merge.pdf, EA1111-25471_frontmatter.pdf, 
> PDFsam_merge.pdf, W000005.pdf
>
>
> I have two Bookmark PDFs with Page and Content links which works fine 
> independently. But when i use PDFMergerUtility, though it successfully merges 
> with PDF bookmarks, some of the page and content links are not working.
> Could you please let me know if you have any suggestions.



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