getIndexDataWithoutSystemDB.js

var colls = db.getCollectionNames();
var ret = [];

colls.forEach(function(coll) {
    if (String(coll).startsWith("system")) {
      return;
    }

    var indexes = db.getCollection(coll).getIndexes();
    var stats = db.getCollection(coll).aggregate( [ { $indexStats: { } } ] );
    var len = indexes.length 
    ret.push({ "name": coll, "length": len, "data": stats._batch});
})

printjson(ret)