Merge and Split tool presently require a djvu file, but it's possible to extend it to pdf (obviously with a text layer).
If someone is interested about, I can publish here the simle code needed to update M&S tool.
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@Alex_brollo: Please explain what/in which gadget or application or server "Merge and Split tool" is and follow the structure in https://www.mediawiki.org/wiki/How_to_report_a_bug when creating tasks here. Thanks!
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Match and split is a tool run by Phe-bot, used by many wikisource projects. But perhaps Phabricator is not the right place to discuss its code. I opened a talk here: Extending match do pdf files.
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@Alex_brollo: Please always provide links so no-one has to guess what you refer to. :)
I guess this is about https://en.wikisource.org/wiki/User:Phe-bot which links to https://tools.wmflabs.org/phetools/ .
(I'm a bit confused it is not listed on https://tools.wmflabs.org/admin/tools or https://tools.wmflabs.org/admin/tools#!/maintainer/phe .)