As an example, here's the programs entry from Atlanteans Labyrinth:
[programs]
sleep=_Sleep
upgrade_soldier_defense_0=_Upgrade soldier defense 0
upgrade_defense_0=_Upgrade soldier defense 0 (only for compatibility with old savegames (build13))
upgrade_soldier_defense_1=_Upgrade soldier defense 1
upgrade_defense_1=_Upgrade soldier defense 1 (only for compatibility with old savegames (build13))
upgrade_soldier_hp_0=_Upgrade soldier health 0
upgrade_hp_0=_Upgrade soldier health 0 (only for compatibility with old savegames (build13))
upgrade_soldier_evade_0=_Upgrade soldier evade 0
upgrade_evade_0=_Upgrade soldier evade 0 (only for compatibility with old savegames (build13))
upgrade_soldier_evade_1=_Upgrade soldier evade 1
upgrade_evade_1=_Upgrade soldier evade 1 (only for compatibility with old savegames (build13))
As we can see, half of the programs are merely for compatibility reasons for older save games. Since build 13 is quite some time ago, I don't know how this has worked in recent releases. Regardless, since the change to eris breaks all compatibility anyways these entries can be removed. Is it sufficient to clean up the conf-files, or are there parts of the source code looking for these too?
Yes, we do not give any compatibility guarantees till b19 is out of the door. Everything that mentions compatibility can be killed on sight.
I do not know if some code is looking for these entries, but starting with removing those and then killing all code that complains is probably a workable solution.