Use --manifest-file=somefile.d to output the dependency manifest.
This file will contain a list of files which were read by protoc as part
of creating the output files.  It doesn't include the plugin inputs if
plugins are used, that could be a later extension.
The manifest file is in the format <output file>: <input files>.  The
manifest file format only allows you to specify one output file, which
isn't a problem as it's used to detect input changes in order to detect
when to rerun the protoc command.  The output file used in the manifest
is the manifest filename itself; to use this in ninja you should declare
the manifest file as the first output as well as the depfile input.