You can use gulp-flatten
https://www.npmjs.com/package/gulp-flatten
app
├── logo
│ └── logo.styl
└── sidebar
└── sidebar.styl
var flatten = require('gulp-flatten');
gulp.src('app/**/*.styl')
.pipe(flatten())
.pipe(gulp.dest('dist/'));
dist
├── logo.styl
└── sidebar.styl