To markup or edit a pdf document there are a few options. A particularly full featured option is to use libreoffice which essentially combines pdf editing with the full power of the Libre Office suite. The application can be invoked with libreoffice from the command line:
$ libreoffice mydoc.pdf
After editing the document simply export it as a pdf file by clicking the PDF button in the toolbar or from the File menu, Export As, Export Directly as PDF.
On exiting libreoffice itself an option to save the file is presented. This will save the document into an OpenDocument Draw format file with the extension odg which is an open standard Libre Office file format. It is not ususally necessary and so choose Don’t Save.
The application evince has the option to add notes or to highlight text to a pdf document.
The package flpsed is a PostScript markup tool which can import pdfs that can then be edited and exported back to a pdf document.
To fill in pdf based forms load the form into the Brave browser (e.g., by browsing to file://home/kayon/documents/applicaiton.pdf) and you can fill the form in and save it.
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