java.io.IOException: Cannot run program "...": java.io.IOException: error=2, No such file or directory

The ProcessBuilder constructors require each argument of the external program to be separate (in the form of an array or List of Strings). The first exception message you got,

Cannot run program "/usr/bin/libreoffice --headless --convert-to pdf:'writer_pdf_Export' --outdir /home/develop/tomcat/mf/ROOT/private/docs/0 /home/develop/tomcat/mf/ROOT/private/docs/0/35_invoice.fodt"

is not complaining that it can find a program named /usr/bin/libreoffice. It is complaining that it can not find a program with the very long and peculiar name "/usr/bin/libreoffice --headless --convert-to pdf:'writer_pdf_Export' --outdir /home/develop/tomcat/mf/ROOT/private/docs/0 /home/develop/tomcat/mf/ROOT/private/docs/0/35_invoice.fodt", because you concatenated the arguments into one String.

Instead of

command.add("--convert-to pdf:'writer_pdf_Export' --outdir " + getDestinationDirectory(order) + " " + getInvoiceFilename() + ".fodt")

and such like, split each of the arguments into its own call to List.add

command.add("--convert-to");
command.add("pdf:writer_pdf_Export");

command.add("--outdir");
command.add(getDestinationDirectory(order).toString());

command.add(getInvoiceFilename() + ".fodt");

Note that there are no apostrophes around "writer_pdf_Export" since those are shell meta-characters and are not required when you're constructing an array to pass to exec without an intermediating shell.