Yeah, true.
We have many overrides too, although our latest app started like with Ext 4 developer preview 1.
Our old Ext 2 apps are staying on that!
To help with the issue of finding stuff that you have either overridden or copied from src and tweaked (since sometimes you just have to) I wrote a simple function to help:
Code:
/**
* Function that logs a warning in the console if the lastCheckedVersion of a function
* is less than the current Extx version.
* Should be wrapped in <debug> tags.
* @param {String|Number} lastCheckedVersion The version to check against the current Ext version.
* @param {Function} func The function that we are being called from.
*/
Altus.warnIfExtVersionUpdated = function(lastCheckedVersion) {
var currentExtVersion = Ext.getVersion('extjs');
if (!currentExtVersion.match(lastCheckedVersion)) {
if (Altus.Logging) {
Altus.Logging.warn(arguments.callee.caller,
'Method is an override that duplicates code in the framework, so needs checking.',
'Last checked version: ' + lastCheckedVersion,
'Current version: ' + currentExtVersion);
} else {
// Wait for Altus.Logging to be loaded...
Ext.Function.defer(arguments.callee, 10, this, arguments);
}
}
};
Slightly filthy (with the defer), but serves the purpose 
Then use it either at the start of the function where parts of the src have been copied, or in the callback from define, e.g.
Code:
Ext.define('Altus.overrides.button.Button', { override: 'Ext.button.Button',
/**
* Avoid using the horrendous button layout.
* See here: http://www.sencha.com/forum/showthread.php?243089
* @type {String}
*/
componentLayout: 'autocomponent'
},
function() {
// <debug>
Altus.warnIfExtVersionUpdated('4.1.3');
// </debug>
});
I don't imagine you'll get any dev input in this thread, and if you do it won't be until after the conference.
Cheers,
Westy
PS: Good to be back; not posted on the forums in months!