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Knowing the file's _id, you can call update on the FS.Collection instance:
_id
update
FS.Collection
myFSCollection.update({_id: fileId}, {$set: {'metadata.foo': 'bar'}});
If you have the FS.File instance, you can call update on it:
FS.File
myFsFile.update({$set: {'metadata.foo': 'bar'}});