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Unfortunately, the bookmarks bug also exists in the PDF plugin in document-viewer-plugins-4.0+svnr6952. Just compile this plugin (enable the plugin in plugins/pdf/plugin_impl/Makefile.am) from these sources, overwrite /usr/lib/uds/libuds-plugin-adobe.so and open a PDF file. I hope one of the iRex developers can have a look at this.
I did notice something peculiar in plugins/pdf/plugin_impl/document_impl.cpp, lines 465,466:
else if ((start_param.toc_idx = -1) && (end_param.toc_idx = -1)
&& (start_param.toc_idx == end_param.toc_idx))
those assignment operators are probably wrong (I think they should be != instead), but changing that doesn't fix the bookmark problem
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