In SugarCRM, you can create your custom modules (e.g. MyModule) and they are kept in /modules just like stock objects, with any default metadata, views, language files, etc. For a custom module MyModule, you might have something like:
/modules/MyModule/MyModule.class.php
/modules/MyModule/MyModule.php
/modules/MyModule/language/
/modules/MyModule/metadata
And so on, so that everything is nicely defined and all the modules are kept together. The module becomes registered with the system by a file such as /custom/Extension/application/Include/MyModule.php with contents something like:
<?php
$beanList['MyModule'] = 'MyModule';
$beanFiles['MyModule'] = 'modules/MyModule/MyModule.php';
$moduleList[] = 'MyModule';
Obviously, the $beanFiles array references where we can find the base module's class, usually an extension of the SugarBean object. Recently I was advised that we can adjust that file's location for the sake of customization, and it makes sense to a degree. Setting it like $beanFiles['MyModule'] = 'custom/modules/MyModule/MyModule.php'; would allow us to access the base class via Module Loader even if the security scan tool prevents core file changes, and this would also allow us to not exactly extend, but replace stock modules like Accounts or Calls, without modifying core files and having system upgrades to wipe out the changes.
So here's my question: what is the best practice here? I've been working with SugarCRM pretty intensely for several years and this is the first time I've ever been tempted to modify the $beanFiles array. My concern is that I'm deviating from best practice here, and also that somehow both files modules/MyModule/MyModule.php and custom/modules/MyModule/MyModule.php could be loaded which would cause a class name conflict in PHP (i.e. because both classes are named MyModule...). Obviously, any references to the class would need to be updated (e.g. an entryPoint that works with this module), but am I missing any potential ramifications?
Technically it should be fine, but I can see how it could be possible that both the core version and your version could conflict if both are referenced. It all depends on the scenario, but I prefer to extend the core bean and find somewhere in the stack where I can have my custom version used in place of the core bean. I wrote up an example a couple of years ago here: https://www.sugaroutfitters.com/blog/safely-customizing-a-core-bean-in-sugarcrm
For most use-cases, there's a way to hijack Sugar to use your bean at a given point.
If you can't get around it you can always grep to see where the core module is explicitly being included to ensure that there won't be conflict down the road.