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> what advantages does having the RDBMS be the prime metaphor over the file system?

Easy queryability and easy joining of data across a whole datacenter.

This makes it easy to think about system data across all sorts of boundaries that the file metaphor makes somewhat cumbersome.

> This makes it easy to think about system data across all sorts of boundaries that the file metaphor makes somewhat cumbersome.

while file metaphor became big in previously SQL domain of data processing, i.e. the whole ecosystem of HDFS and everything on top of it

At the end of the day, almost everyone queries those HDFS files with query language using Pig, Hive, Presto, etc.