I just noticed that stores config http://docs.sencha.com/extjs/6.0/6.0.2-classic/#!/api/Ext.app.Controller-cfg-stores on Ext.app.Controller is not looking in the right path (happens the same with views config).
e.g
Ext.define('MyApp.controller.Menu', {
    extend: 'Ext.app.Controller',
    stores: ['Menu']
...
});
this will look for
http://localhost/myapp/app/controller/store/Menu.js?_dc=20160607211025
notice the controller folder
instead of
http://localhost/myapp/app/store/Menu.js?_dc=20160607211025
At the beginning I thought this was a configuration issue specific to one of my projects but then got the same thing on a different project.
I am using ExtJs 6.02
I know I can use the full class name like MyApp.store.Menu but then the getter would be very ugly. (This is happening on a huge code base that I just upgraded so using the full class name would be my last resource).
Has someone faced this issue ?
I've found the reason (bear with me):
https://docs.sencha.com/extjs/6.0/6.0.2-classic/source/Controller2.html#Ext-app-Controller
look at:
onClassExtended -> Controller.resolveNamespace -> Ext.app.getNamespace
Those are the important ones, once the namespace is resolved there is a call to process dependencies:
Controller.processDependencies(proto, requires, namespace, 'store', data.stores);
I researched this and Ext.app.getNamespace is identical in ext 5 and 6
so why is it in ExtJs 5
Ext.getNamespace("MyApp.controller.SomeController"); // returns MyApp
and on ExtJs 6
Ext.getNamespace("MyApp.controller.SomeController"); // returns MyApp.controller
The reason is found by console.log Ext.ClassManager.paths there is now a new entry that corresponds to MyApp.controller

previously there was no key for MyApp.controller (ZHT.controller)
And what Ext.getNameSpace does is look for the 'deepest prefix' as you can see here http://docs.sencha.com/extjs/6.0/6.0.2-classic/source/Util.html#Ext-app-Util
[update] So one thing that can be done is to override the static method resolveNamespace like this:
  statics: {
    resolveNamespace: function(cls, data) {
            var Controller = Ext.app.Controller,
                namespaceRe = cls.prototype.isProfile ? Controller.profileRegex : Controller.controllerRegex,
                className, namespace, match;
            /*
             * Namespace resolution is tricky business: we should know what namespace
             * this Controller descendant belongs to, or model/store/view dependency
             * resolution will be either ambiguous or plainly not possible. To avoid
             * guessing games we try to look for a forward hint ($namespace) that
             * Application class sets when its onClassExtended gets processed; if that
             * fails we try to deduce namespace from class name.
             *
             * Note that for Ext.app.Application, Controller.onClassExtended gets executed
             * *before* Application.onClassExtended so we have to delay namespace handling
             * until after Application.onClassExtended kicks in, hence it is done in this hook.
             */
            className = Ext.getClassName(cls);
            namespace = data.$namespace || data.namespace ||
                Ext.app.getNamespace(className) ||
                ((match = namespaceRe.exec(className)) && match[1]);
            //<debug>
            if (!namespace) {
                Ext.log.warn("Missing namespace for " + className + ", please define it "+
                    "in namespaces property of your Application class.");
            }
            //</debug>
            //This is the only change on this override.
            //http://stackoverflow.com/questions/37731213/extjs-6-stores-config-on-ext-app-controller-not-working/37733261#37733261
            if(namespace && namespace.indexOf(".controller") > -1) {
                namespace = namespace.slice(0, namespace.indexOf(".controller"));
            }
            return namespace;
        }
  }
If you know of a better solution please let me know!
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