There are three groups of protos in the respective perfetto/X directories:
trace/: This directory contains all protos that are output-ed by Perfetto when capturing a trace.
config/: This directory contains the configuration passed as input to various parts of Perfetto, such as:
ipc/: This directory contains the definition of the IPC surface between the Perfetto components (Producer, trace daemon and Consumer(s)). This is relevant only in some Perfetto build configuration (i.e. in Android but not in Chrome).