You need to do two things here (the details are in the useful thread I linked you to, so please read).
- Configure requirejs so that when you declare modules (e.g. "jquery", "bootstrap"), requirejs can resolve them to actual files, minified or otherwise.
- Shim bootstrap by specifying jquery as its dependency, so that jquery is loaded before it.
To accomplish these, make a call to requirejs.config({...}) with the appropriate options (here is an example). The use case there is exactly the same as yours: jquery is specified as a bootstrap dependency by shimming bootstrap. There you will also see an example of how to tell requirejs where your files are (this is accomplished via the paths property). Note how the .js extension is not explicitly specified there; do the same.
Needless to say, configuring requirejs can get complicated, but the basic idea is there, configure it by specifying the base directory and where the files are to be found, then shim non-AMD modules. An important thing to be aware of is that bootstrap is going to be what's called a declarative module, which means that it's only used for its side-effects (viz. for what changes it makes to $).
requirejs.config. Did you read the top answer I linked to above?