1. You can call 3rd Party APIs either from javascript, plugins or custom workflow activities.
2. To get the case details there are many ways. You can pass the Guid of the case and retrieve information via javascript from the CRM web api. Or you can build your early bound classes and access case details in C# (plugins/custom workflow activities)
3. You can use Visual Studio, Rest Builder and CRM Work Bench to build fetch xml queries and more.
4. You javascripts and html pages will be kept in side web resources. Plugins and custom work flow activities needs to be registered using the plugin registation tool and they will end up in CRM eventually. Solutions can be used to package these items.
Sachith Chandrasiri