I'm using pdftk multistamp on a server for adding custom page numbering, page headers and page footers to big (500-1200 pages) PDF files. I do this by counting number of pages in the input, creating suitable empty pages with page numbers, headers and footers using LaTeX and then use pdftk multistamp to combine the original PDF and the PDF with pages, headers and footers.
However, pdftk is based on libgcj (and gcj) and gcj is no longer maintained and has already been removed from GCC 7.1. As such, pdftk does not have any future as-is.
How to merge/combine PDF files in the future? I really would want to keep hyperlinks between pages working in resulting PDF files and metadata as much as possible.
I started a Java port of pdftk a few months back; at this point it should have the same functionality as the C++ version but a lot more testing is needed. If you want to give it a try, check https://gitlab.com/pdftk-java/pdftk and file a bug report when it breaks.