The proto_library.proto_source_root attribute is going away in favor of the more flexible proto_library.strip_import_prefix and proto_library.import_prefix.
In order to migrate your BUILD files, replace proto_source_root with strip_import_prefix: since the only allowed value of that attribute is the package the rule is in, simply replace the name of the attribute and prepend / to its value. For example, the rule (necessarily in foo/bar/BUILD):
proto_library(name="proto", srcs=["proto.proto"], proto_source_root="foo/bar")
Needs to be migrated to:
proto_library(name="proto", srcs=["proto.proto"], strip_import_prefix="/foo/bar")