Remove "old pipeline" modules.
Remove old `gmt vcf vcf-maker` tools.
Remove `gmt germline vcf-maker`.
Test that we really ran the command wrappers.

The first test would necessarily have done so to get the count to 1,
but the second could have done nothing at all.
Whitespace.
Check existence of command earlier so we reach friendly error message.
Whitespace.
Whitespace.
Whitespace.
Check results of command execution.
Whitespace.
Check results of command execution.
Whitespace.
Whitespace.
Add true value.
Check results of command execution.
Whitespace.
Whitespace.
Check results of command execution.
Whitespace.