Most programming projects are kept afloat by the best programmers on the team.
I don't understand this sentence. I found "afloat" to have meaning of "floating on water" which does not suit in this sentence. Am I using the wrong definition?
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Yes, you are looking at the wrong definition.
6. free of major trouble, especially financially solvent:
to keep a venture afloat.
The best programmers keep the projects viable. Without them, the projects would be in trouble and likely fail.
You can think of afloat metaphorically by considering the project to be a ship. If it is afloat, then it is safe. If it is not afloat, then it is sinking and in serious trouble.