From the gs pack­age in Ubuntu:

gs –dBATCH –dNOPAUSE –q –sDEVICE=pdfwrite –sOutputFile=outputMerged.pdf file1.pdf file2.pdf

jPdf Tweak, the “Swiss Army Knife for PDF files”, is also a great tool and run out of the box with Java but it might be faster just using the above com­mand rather than brows­ing through jpdftweak’s GUI.