There is an idea to create a branch in which the versioning of files will be entered to enable upgrades.

For files, accept the version of the type 0.4.12.x
Or create a branch based on 0.4.11 call it 0.4.11 Extended Support
To replace files with "hot" need to replace actions on behalf of "SYSTEM"? And for those files that can not be replaced without rebooting:
A: micro live system
B: function in the loader allowing to replace files
C: what to do if you need to update the bootloader?
As an option, you can put a new version of the bootloader in a temporary folder, load the old bootloader into RAM, replace the old bootloader files on the disk, reboot and start up with the new bootloader
or option A with a micro live system
or a hybrid version with a full live system on the HDD and installed