Remove checked-in generated files and use build-time gen ones

Pre-requisite step for http://go/perfetto-libprotobuf
(get rid of libprotobuf runtime dependency).
This change keeps some checked-in headers as proxy shims
(e.g. include/core/data_source_config.h has only
#include ".../data_source_config.gen.h")
This is to handle potential reverts of the chromium roll
more easily. They will be removed in a follow-up.

Bug: 132880619
Test: CI
Change-Id: I2d8c391b060dac37209a640e269e13ae34e8981f