1- We needed to modify a "core file" (one of the notification mail templates)

The templates (i.e. everything you see in the app/views directory can be overridden by a plugin. Just create a new file with the same path and name as the file in the core in your plugin. It will then automatically take precedence. Note that you should then closely observer changes to these files in the ChiliProject core to make sure your plugin remains compatible.

2- We have the code in an internal subversion server

While ChiliProject core uses git (and prefers Pull Requests on Github for contributions), you don't need to use Git for your internal development. If you have any proposed changes, you can also just open an issue and attach a patch. See our Contribute page for more details.

Ok, thanks!
There is one more thing.
My plugin has a hook to operate on incoming mails. We have modify the mail_handler_controller to add our hook. Is this acceptable or there is a better way?

Thanks!