UPDATE

Checking once more your code, there is a bunch of repeted code you should turn into methods. For instance, this whole part

var dir = "";
if (typeof source[i].dir == "undefined") {
    // default = js-common
    dir = sourceFiles.staticJsCommon();
} else if (typeof source[i].dir == "js-common") {
    dir = sourceFiles.staticJsCommon();
} else if (typeof source[i].dir == "css-common") {
    dir = sourceFiles.staticCssCommon();
} else if (typeof source[i].dir == "img-common") {
    dir = sourceFiles.staticImgCommon();
}

should become one method with one param

var dir = sourceFiles.handleFileDir(source[i].dir)

and all the methods below

staticRoot : function () {
    if (typeof $ms.STATIC_TOP_ROOT !== "undefined") {
        return $ms.STATIC_TOP_ROOT;
    } else {
        return window.location.origin ? window.location.origin + '/' : window.location.protocol + '/' + window.location.host;
    }
},
staticJsCommon : function () {
    if (typeof $ms.STATIC_JS_COMMON !== "undefined") {
        return $ms.STATIC_JS_COMMON;
    } else {
        return window.location.origin ? window.location.origin + '/' : window.location.protocol + '/' + window.location.host + "/js-common";
    }
},
staticImgCommon : function () {
    if (typeof $ms.STATIC_IMG_COMMON !== "undefined") {
        return $ms.STATIC_IMG_COMMON;
    } else {
        return window.location.origin ? window.location.origin + '/' : window.location.protocol + '/' + window.location.host + "/img-common";
    }
}

are really only one method. Could be something like

handleFileDir : function (pathPart) {
    // decide on type ref and define the var
    var typeToCheck = function (_path) {
        if (_path.indexOf("js") > -1) return "STATIC_JS_COMMON";
        if (_path.indexOf("css") > -1) return "STATIC_CSS_COMMON";
        if (_path.indexOf("img") > -1) return "STATIC_IMG_COMMON";
        return "STATIC_TOP_ROOT";       
    }(pathPart);
    
    if (typeof $ms[typeToCheck] !== "undefined") {
        return $ms[typeToCheck];
    } else {
        return window.location.origin ? window.location.origin + '/' : window.location.protocol + '/' + window.location.host + pathPart;
    }
}

Always be suspicious of code smell when parts of your code look alike so much...

Well, I did not check or run the whole code, but I do see lots of code repetition that you should avoid. For example, returning a windows.location should use a help function.

So these kind of lines

return window.location.origin ? window.location.origin + '/' : window.location.protocol + '/' + window.location.host + "/js-common";

could be:

return buildURL("/js-common")

Well, I did not check or run the whole code, but I do see lots of code repetition that you should avoid. For example, returning a windows.location should use a help function.

So these kind of lines

return window.location.origin ? window.location.origin + '/' : window.location.protocol + '/' + window.location.host + "/js-common";

could be:

return buildURL("/js-common")

It's not only about the size of the code, it is mainly for other reasons, like, reusability, readability, maintainability, etc. Some times we prefer more size if it comes with one or more of these pros.