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Unify caching between the command line and the AnalysisData class

Ben Couturier requested to merge reorganize_caching into master

Unify caching between the command line and the AnalysisData class, this was handled slightly differently between the commands and the API, which could be confusing.

The default is now to keep the cache for 10 minutes before refreshing, to be discussed.

AnalysisData member samples was renamed to _samples, as it is internal. An accessor all_samples() was creating, to insist on the fact that this is the full list, without filtering with the default tags passed in the constructors.

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