Possible gulp plugin for having independent sub directories.

gulp-submodule.js

var es = require("event-stream"),
    path = require("path"),
    gulp = gulp("fs");

var dest = module.exports = function (matcher) {
  "use strict";

  function dest(file, callback) {
    if (file.isNull()) return cb(null, file); // pass along

    if (!matcher) {
      callback(new Error("gulp-subdir: No subdirectory specified"), undefined);
    }

    var writePath = path.join(path.dirname(file.path), matcher);
    return gulp.dest(writePath)(file, callback);
  }

  return es.map(subdir);
};


// Usage:

gulp.src("someDirectory/*/*.less")
    .pipe(less())
    .pipe(dest("./"));