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I would like to do some basic editing on existing PDF file. More specifically:

• Add chapters/bookmarks


• Change page numbering

However, I cannot find any tool, GUI or command line, which would offer this functionality. Is there any free-open alternative tools?

I use pdftk mainly. But here are some others to consider:

pdfsam (PDF Split and Merge): "pdfsam is an open source tool (GPL license) designed to handle pdf files"

PDFJam "A small collection of shell scripts which provide a simple interface to much of the functionality of the excellent pdfpages PDF file package (by Andreas Matthias) for pdfLaTeX." (You can also use pdfLaTeX directly.)

jPDFTweak: "jPDF Tweak is a Java Swing application that can combine, split, rotate, reorder, watermark, encrypt, sign, and otherwise tweak PDF files."

Inkscape: is a vector graphics editor that can both import PDF pages into its native SVG format, and also export as PDF.

Calibre: Open source ebook management software that can convert PDFs to other formats, and manipulate them in other ways. Comes with command line tools such as pdfmanipulate which can be useful.

Ghostscript of course can do a lot of things with PDF files too.

I know two programs for manipulating PDFs under Linux:

PDEedit "PDFedit is a free open source pdf editor and a library for manipulating PDF documents, released under terms of GNU GPL version 2. It includes PDF manipulating library based on xpdf, GUI, set of command line tools and a pdf editor."

and
pdftk "If PDF is electronic paper, then pdftk is an electronic staple-remover, hole-punch, binder, secret-decoder-ring, and X-Ray-glasses. Pdftk is a simple tool for doing everyday things with PDF documents."

The only way I found to add page numbers to a PDF was with LaTeX:

Create a file /usr/local/bin/add-page-numbers.tex

documentclass[8pt]article
usepackage[final]pdfpages
usepackagefancyhdr

topmargin 70pt
oddsidemargin 150pt

pagestylefancy
rfootLargethepage
cfoot
renewcommand headrulewidth0pt
renewcommand footrulewidth0pt

begindocument
includepdfsetpagecommand=thispagestylefancy
includepdf[pages=-]input.pdf
enddocument

And a file /usr/local/bin/pdf-numbers

#!/bin/bash
name="$1%.pdf-numbers"
wd="$(pwd)"
dir=/tmp/pdf-numbers
mkdir -p "$dir"
cp "$1" "$dir/input.pdf"
cd "$dir"
pdflatex --jobname "$name" /usr/local/bin/add-page-numbers.tex > /dev/null
mv "$name.pdf" "$wd"
rm -r "$dir"

Make the latter file executable, and run it with

 pdf-numbers example.pdf

It will create a pdf file called example-numbers.pdf (and overwrite it if it already exists!).

pdfimport for openoffice is a good alternative to edit PDF documents and re-export to PDF or save to another format. The imported PDF can be edited with OpenOffice Draw.

latex with the pdfpages packages can do most of these things.

Specifically on how to add bookmarks, see http://michaelgoerz.net/blog/2011/04/pdf-bookmarks-with-latex/