Configure your .cyclopt.json to ignore files and folders. This is what we use as our basis. Supports minimatch patterns https://github.com/isaacs/minimatch#usage

.cyclopt.json

{
    "ignore": [
      "**/deps/**",
      "**/node_modules/**",
      "**/thirdparty/**",
      "**/third_party/**",
      "**/bower_components/**",
      "**/vendor/**",
      "**/vendors/**",
      "**/**-min-**",
      "**/**-min.**",
      "**/**.min.**",
      "**/**jquery.?(ui|effects)-*.*.?(*).?(cs|j)s",
      "**/**jquery-*.*.?(*).?(cs|j)s",
      "**/prototype?(*).js",
      "**/mootools*.*.*.js",
      "**/dojo.js",
      "**/MochiKit.js",
      "**/yahoo-*.js",
      "**/yui*.js",
      "**/ckeditor*.js",
      "**/tiny_mce*.js",
      "**/tiny_mce/?(langs|plugins|themes|utils)/**",
      "**/MathJax/**",
      "**/shBrush*.js",
      "**/shCore.js",
      "**/shLegacy.js",
      "**/modernizr.custom.?(*).js",
      "**/knockout-*.*.*.debug.js",
      "**/extjs/*.js",
      "**/extjs/*.xml",
      "**/extjs/*.txt",
      "**/extjs/*.html",
      "**/extjs/*.properties",
      "**/extjs/.sencha",
      "**/extjs/docs/**",
      "**/extjs/builds/**",
      "**/extjs/cmd/**",
      "**/extjs/examples/**",
      "**/extjs/locale/**",
      "**/extjs/packages/**",
      "**/extjs/plugins/**",
      "**/extjs/resources/**",
      "**/extjs/src/**",
      "**/extjs/welcome/**",
      "**/*bootstrap*.js",
      "**/*jquery*.js",
      "**/test*/**/*",
      "**/grunt/**/*",
      "**/example*/**/*",
      "**/[Gg]ulp[Ff]ile.*",
      "**/[Gg]runt[Ff]ile.*",
      "**/*spec.js",
      "**/*spec*/*",
      "**/dist/**/*",
      "**/build/**/*",
      "**/*benchmark*/**/*",
      "**/*dist*/**/*",
      "**/*plugins*/**/*",
      "**/*build*/**/*",
      "**/*vendors*/**/*",
      "**/*node_modules*/**/*",
      "**/*bower_components*/**/*",
      "**/*build.js",
      "**/*bundle.js",
      "**/*tests?.js",
      "**/*webpack*"
    ]
  }