Eliminate all data exchange via disk-files in the later stages

[bjclavijo]

I clutters the disk, but also makes functions more difficult to debug, understand, etc.

[ljyanesm]

There are no temporary files for data exchange left.

Exceptions:

• step3 reuses the output from step2 to build the initial graph without holding all the data in memory.
• step4 needs to reload the graph to transform into larger K.