The problem of automatic code merging (2014)

I understand this is a slightly contrived example, but if you work against the system, usually the system will work against you.

I think the problem here stems from improper use of version control.

It basically sums up to not trusting the version control system and keeping a 'backup' with the rest of the code, dead code should be eliminated, if you ever need it again restore it from VCS.