After 1,5 years of working on Sharepoint I realized completely that way we are doing Sharepoint is NOT SUPPORTED... which is not a big surprise.
This kind (Sharepoint) of development isn't intended to live the same way as ASP.Net development:
Here is an article to MUST read before to start invent a vehicle to drive everybode crazy)
To be short, after Prod release - you can't change the structure of data or event master page through the same way as you did development (site template or list feature), you should switch to use the Sharepoint Designer or get in touch with a feature stapling
The real hands-on "how to use the feature stapling" - Feature Stapling in Use