How to organize CSS,JS and other files into ASP MVC 4

Question

I am totally new to ASP.NET MVC 4 as I was developing into PHP (Laravel) and the way to organize things is usually something like a "public" folder which would then be separated into css, img, js, lib, and so on.... which is the way I prefer to organize my files...Trying to follow this into ASP MVC 4, and I found and read this question that is similar to what I want achieve.
organizing custom javascripts in asp.net mvc 4

I did it the way they said and added my custom JS files and added them in the Bundle, it compile and also run fine but the problem I have is that inside the Solution Explorer all the files that I moved are showing with an exclamation mark and also my newly created folders (directly in file explorer, not doing it through VS) are not showing by default, they are for some reason hidden, which I can see with Show All Files. I made sure that they exist inside the Bundle but then my Solution Explorer does not get refreshed. I am trying to make a structure that looks the following:

Contents
    img
        ui-icons.png
    css
        bootstrap
            bootstrap.css
            bootstrap.min.css
Scripts
    lib     
        bootstrap
            bootstrap.min.js
            bootstrap.js
        jquery
            jquery.js
            jquery.min.js
            jquery.ui.js
            jquery.ui.min.js
        modernizr
            modernizr.js
    custom
        mycustom.js
        mycustom2.js

I am not crazy about dumping everything inside the same folders (Content & Scripts), including my custom files in between some official libraries. I know using directly the File Explorer is probably not the best way to go, but then what would be the official way of configuring these... and actually does my structure make sense into ASP MVC4?
EDIT
My question is more related to why after creating and moving the files like jquery and others into a Scripts/lib folder, my Solution Explorer is still showin these files under Scripts but with an exclamation marks as saying file not found (of course since I moved them). Why it doesn't reflect exactly what I see in File Explorer? Apart from editing the Bundles is there anything else I'm suppose to do so that my Solution Explorer is up to date with reality??? and why are my created folders not showing in Solution Explorer, why do I have to click on Show All Files to see them? The commmand Create New Folder is not even enable as an available command, that's why I have done these folders directly in File Explorer...but why?

Answer 1

Frankly, you can organize your MVC project however you see fit. If there's anything close to an "official" way to organize your web files, it would be how the default Visual Studio MVC4 template organizes them:

• Content (CSS files and related image files)
• Images (general image files)
• Scripts (JavaScript files)

If you're more familiar with another sort of organization or are part of a team that would prefer another organization, then go for it. (Though in that team scenario, make sure all the team members follow the same organization rules!).

Edit:

To alter the folder structure that the MVC template provides using the Solution Explorer, right-click on the folder in which you want to add a subfolder (this includes the project name, for project-level folders), and then select Add and then Add Folder from the pop-up menu that appears.

If you want to move around files that are already in your solution to another location within the solution, you should move them around using the Solution Explorer, not Windows Explorer, as you'll otherwise get the behavior you are experiencing, where Visual Studio does not know where you moved them. You can click and drag files around, right-click and copy and paste, etc.

If you need to add pre-existing files to your solution (say, to include a set of custom scripts), you can copy the files to the appropriate project folder using Windows Explorer. Then, in Visual Studio, highlight the project that corresponds to where you moved them, and press the Show All Files button in the Solution Explorer toolbar - this will show the files you copied in Windows Explorer, which otherwise won't be listed in Solution Explorer tab. Lastly, highlight the new files, right-click, and select the Include in Project option from the pop-up menu.

One final pointer: if you need to add a specific JavaScript library to your project, the easiest way to do so would be to use the NuGet package manager, rather than to download and add the files in Windows Explorer. This option is found in Visual Studio in the Tools menu, under Library Project Manager --> Manage NuGet Packages for Solution. Not all JavaScript libraries will be available this way, but the most popular ones are.