Check the following contrast between the past perfectThe aspect expressing completion. E.g.: He’s finished university. and the past perfect continuousThe aspect expressing duration, formed with be + verb-ing. E.g.: What are you doing?. The former emphasisSpecial importance or attention given to something. E.g.: All I wanna do is have some fun.es completionA concept, related to the perfect aspect, expressing that an action has finished. E.g.: He’s finished university. while the latter emphasises the activity or its durationA concept, related to the continuous aspect, expressing that an action is in progress. E.g.: What are you doing? .

By 6 he had eaten all the food. (there was nothing left)
He put down the fork he had been eating with and left the table.

Diagrams

Past perfect continuous for past habits
Past perfect continuous Present simple to express past