Its a new term for the BF community that was coined after the release of BF2: Special Forces. This term dates back to November 22, 2005
<bit of sarcasm>While I know you were kidding, all BF releases, including 1942 used the term "Vanilla" to denote the original manufacturer version. </bit of sarcasm>
Vanilla is a term used for an "off the shelf" version of software mate . Companies supply a standard version and any modifications that their customer base wants then make it bespoke .
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