Move Update protobuf message to Api namespace
Issue #2: Remove Query protobuf message

Remove the Query protobuf message. It is replaced by the
internal Query data structure.

This also changes the API: kCqQuery messages do not
contain a Query field anymore; the fields of Query have
been added to CqQuery itself.
Remove Request.proto file

The contents of Request.proto have been merged
into Api.proto and Config.proto by previous commits.
Log submit() and commit() to write-ahead log

This is the first step of resolving issue #6.
What is left TODO is replaying the write-ahead log
in case of a crash.