[m-dev.] stop generating .dep files using module_dep_file_v1 format

[Zoltan Somogyi]

While working on the attached diff, I saw that we have not yet
fully switched to module_dep_file_v2: we use v1 or v2 depending
on whether a list is empty or not. Since using v1 gains us nothing
other than not having to write out, and then read in, a single empty list,
I propose that from now on, we should always write out .dep files
using v2, because it will make the backward compatibility arrangements
of any future v3 so much easier. Any objections?

Note: v2 was introduced in 2014, so compatibility with mmc
versions that don't understand v2 is not an issue.

Zoltan.
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