Factor-bundle and browserify-shim don't play well together

We were using browserify with browserify-shim to be able to use jQuery with a few plugins. So far so good. At this time we were creating another bundle for dependencies common across all pages, manually specifying them.

We then discovered and decided to use factor-bundle to factor common dependencies in a better way. The result was very good in terms of file size, but shims provided by browserify-shim disappeared. Since jQuery and its plugins are used in several pages, they're successfully factored out with factor-bundle, but they're produced without the shims. The problem is that jQuery plugins rely in `window.jQuery` that's no more available since there's no more shim.

We ended up `require`ing jQuery manually in the HTML and expose it, with `var jQuery = require("jquery")`. We would love factor-bundle to work with browserify-shim (or the opposite, whatever).

My understanding is that since factor-bundle is a plugin that act at the bundle level, it may not call it properly. But in our setup, it successfully apply the `reactify` transform (we use React.js with JSX syntax). So I suppose it's not a problem of factor-bundle not using transforms at all, but a specific incompatibility between factor-bundle and browserify-shim. However I couln't determine the problem precisely since I'm not familiar at all with the internals of those modules.

For reference in case it helps, here are relevant parts of our package.json and gulpfile (some parts are skipped to focus, it may look inconsistent/weird) :

**package.json**

``` json
"browserify": {
"transform": [
"reactify",
"browserify-shim"
]
},
"browser": {
"jquery": "./node_modules/jquery/dist/jquery.js",
"twitter-typeahead": "./node_modules/typeahead.js/dist/typeahead.bundle.js",
"magnific-popup": "./node_modules/magnific-popup/dist/jquery.magnific-popup.js"
},
"browserify-shim": {
"jquery": "$",
"slick-carousel": {
"depends": [
"jquery"
]
},
"twitter-typeahead": {
"depends": [
"jquery"
]
},
"magnific-popup": {
"depends": [
"jquery"
]
}
}
```

**gulpfile.js**

``` js
function browserifyPages() {
var pages = fs.readdirSync("./pages");

var b = browserify(pages.map(function (p) {
return "./pages/" + p;
}), BROWSERIFY_ARGS);
b.require("jquery");

b = minifyBundle(b); // using minifyify
return b.plugin("factor-bundle", {outputs: pages.map(function (p) {
return JS_DST_DIR + "/" + p;
})});
}

function browserifyCommonJs() {
var b = browserify("./common/header.js", BROWSERIFY_ARGS);
b.external("jquery");
return minifyBundle(b);
}
```

Hope this helps identify the problem. Thanks in advance.

(Let me ping browserify-shim people : @thlorenz and @bendrucker. In case I shouldn't, sorry guys !)