Meteor 1.1 ships with support for MongoDB up to version 3, and you should use Meteor in the production of the MongoDB 3.0 database without serious problems.
However, they decided to leave branch 2.6 in relation to the version of Mongo that comes with the Meteor tool, and wait until Mongo 3.0 is mature enough before including it in the official Meteor releases.
This means that Meteor automatically updates the internal MongoDB tool, but at its own pace.
The local Mongo environment that comes with the Meteor development tool is different from the actual Mongo deployment that you usually use in production, and you do not need the 2 versions to be the same.
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