Using a parameter file for filter option of libav (or ffmpeg)
You can use the -filter_script option:

$ ffmpeg -i input -filter_script filtering -codec:a copy output.mkv


In this example, filtering is a file with the filtergraph.

$ cat filtering 
scale=640:-1,negate


I believe this only works for simple filtergrahps that contain exactly one input and one output.

Libav stuff (avconv and their fake, so-called "ffmpeg" version) is buggy. You can simply download a recent Linux build of ffmpeg from FFmpeg or follow a step-by-step guide to compile ffmpeg.