You could try using this to exclude these files in Gulp
gulp.task("CI-Prepare-Package-Files, function (callback) {
var excludeList = [
config.websiteRoot + "\\bin\\{Sitecore,Lucene,Newtonsoft,System,Microsoft.Web.Infrastructure}*dll",
config.websiteRoot + "\\compilerconfig.json.defaults",
config.websiteRoot + "\\packages.config",
config.websiteRoot + "\\App_Config\\Include\\{Feature,Foundation,Project}\\*Serialization.config",
config.websiteRoot + "\\App_Config\\Include\\{Feature,Foundation,Project}\\z.*DevSettings.config",
"!" + config.websiteRoot + "\\bin\\Sitecore.Support*dll",
"!" + config.websiteRoot + "\\bin\\Sitecore.{Feature,Foundation,Habitat,Demo,Common}*dll"
];
console.log(excludeList);
return gulp.src(excludeList, { read: false }).pipe(rimraf({ force: true }));
});