I was recently asked by a user to help with merging and splitting multiple PDF files. I’m sure Adobe Acrobat could handle something like this, but I’m not that familiar with Acrobat and my user couldn’t afford the full version of Acrobat. Being a command line junky, I looked for something I could run in a terminal window. The first application I found was pdftk. If you’re running a Debian based distribution, just use apt-get to install pdftk. The command to merge multiple PDF files is really simple, and goes something like this:
pdftk file1.pdf file2.pdf file3.pdf cat output out.pdf
pdftk worked fine for a couple files at a time, but then my user wanted 50+ pdf files merged into one file. I tried the following:
pdftk file*.pdf cat output out.pdf
The good news is pdftk merged all of the files, the bad news is the pages were out of order. I’m sure there’s a way to make sure the files merge according to a specific order. However, my user had a deadline fast approaching, so I had to find something else. I did some more searching and found a gem of an application called PDF Split and Merge (pdfsam). pdfsam is a java app, so it will run on Linux, MacOSX, or Windows. I ran pdfsam on my Linux box by using the following command:
java -jar /pathwhereyouunzipped/pdfsam-1.0.0-rc1.jar
Once started, you get this nice GUI interface:

To merge PDF files, simply select the Merge/Extract option, add the files, arrange the files in the order you want by using the “Move Up” and “Move Down” buttons, set your output file, and click the “Run” button. There’s even an option to change the Acrobat version of the output file (6, 7, or 8).

Splitting a PDF file into multiple files is just as easy:

I’d suggest going with pdftk for quick and dirty merging/splitting of a few PDF files. If you have to work with a large number of PDF files, or if you want to set up something you can easily teach a non-techy person to use, I’d recommend going with PDF Split and Merge.