Skip pruning for versions of npm with known issues

The following versions of npm will strip out dependencies installed via git when you run npm prune --production: 5.6.0, 5.5.1, 5.5.0, 5.4.2, 5.4.1, 5.4.0, 5.3.0 (didn't work for other reasons), 5.2.0, 5.1.0

This commit skips the prune step and logs a warning for these versions.