Init-script specified at command (-I/--init-script) should be executed last, so command line trumps default

The facility exposed for init-script is good, however one normally expects command line operations to always trump default operations. This would easily be accomplished by changing the order of operations to be command line last.

As currently written, init-script specified on command line is least preferable, which is odd.

Hi Jeremy,

You make a good point. I’ve raised GRADLE-3039 to fix this.