Improve graph layout for provenance visualization

[remram44]

Right now all the nodes, regardless of whether they are processes, system files or user files, are laid out together.

What I envision is:

• Programs in the middle, one above the other. Also put subsequent executions underneath.
• System files (i.e. package files) on the left
• Other files on the right

The output is in GraphViz DOT format and done by graph.py

[remram44]

Closing after #273 & #269