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replace the original_directory path in the low-level db too

Amir MOHAMMADI requested to merge refactoring_2016 into master

Since some low-level dbs (most of them) accept original_directory and annotation_directory, it is best to replace the paths there too. Here I am assuming that the low-level db exists in BioDatabase._db and have made sure this is the case for all high-level databases. This may not be the solution so I am open to suggestions.

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