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chore: bump protobuf dependency from version 2 to version 3

Dmitry Rodionovrequested to merge
dkr/bump-protobuf into picodata-master

There is an advisory for protobuf crate here: https://rustsec.org/advisories/RUSTSEC-2024-0437.html It says that only version >=3.7.2 is patched.

Before this patch both prost and protobuf backends were supported, for simplicity only protobuf backend is now supported. It is closer to the original version compared to prost.

Most of the changes are caused by renamed getters/accessorts. Now they do not include "get" prefix. So get_index() became just index(). There are some other minor changes in the API that had to be addressed.

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