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Added methods for inserting or overwriting the repository data with files

Mihail Radkov requested to merge feature/GDB-3496-replace-data into master

Additionally added a way to overwrite the data by supplying an array of Quads Added missing context and baseURI parameters for add & addQuads

Included addFile & upload in the transactional repo client.

Added tests and increased the coverage in some existing classes.


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