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The problem is that some packages exist in both the fundamental distribution - and other repositories - with same names, but (newer) with other dependencies, other source code includes and other compilation options, which can and often will break the installation.
So e.g. do not use "opkg upgrade" when non-distribution (e.g. non-OM2009) repositories are included. It often breaks the installation.
Please surround the non-distribution (alien) package install with:
Wish: Actually the package management system should cope with it. The fundamental distribution with a given version number/revision should have higher precedence, and other repositories should have lesser precedence. Maybe the best would be that the package had a distribution list in which it can be "fundamental".
Maybe the package management system should consult a check post (by name and some checksum), so an installer can be informed before installation of the package on the given fundamental distribution:
A package management system should also suggest un-installation of unused packages.
The primarily/non-dispensably packages that the user needs should have been marked - either explicitly or semi-automatically. If the user or an package upgrade make some packages unused, they should be suggested to be uninstalled.