I have added optional auto-assignment of commanders for v2.5. This will happen during the 5-day increment or can be triggered manually on the Commander window. The manual option uses a single button, regardless of whether the automated option is enabled. The automated option is activated by clicking a new checkbox just under the race dropdown on the Commander window.
Auto-assignment takes place for ships, fighter squadrons and ground units without commanders, using the following sequence (Required bonus in parentheses):
Survey ships with R3 requirement (Survey Bonus)
Armed ships with R3 requirement (Crew Training)
Unarmed ships with R3 requirement (Crew Training)
HQ assignments (Ground Unit Training)
Survey ships with R2 requirement (Survey Bonus)
Armed ships with R2 requirement (Crew Training)
Fighter Squadrons (Crew Training)
Unarmed ships with R2 requirement (Crew Training)
Survey ships with R1 requirement (Survey Bonus)
Jump Gate Construction Ships (Factory Production)
Terraformers (Terraforming)
Fuel Harvesters (Mining)
Mining Ships (Mining)
Salvage Ships (Factory Production)
Assault Divisions (Ground Combat)
Armed ships with R1 requirement (Crew Training)
Infantry, Garrison and Engineers (Ground Combat)
Unarmed ships with R1 requirement (Crew Training)
All assignments are accompanied by an Event message, displaying the commander name, the new position and the level of the pre-requisite bonus.
There is no auto-assignment for planetary governors, sector commanders and task force commanders because the required bonuses will depend on player requirements on a case by case basis. At the moment there is also no assignment of staff positions, although I will attempt to add that. None of the above will prevent players from assigning commanders whenever they wish and if you transfer someone with a command, the auto-assign will try to find an officer to fit the vacated command slot during the next update.
The auto-assign also includes the concept of a "Tour", as suggested by sloanjh. The racial Tour length is set on the Commander window and can be from 1 to 60 months. The default is 24. When a commander has spent a tour in the same assignment and is currently on, or in orbit of, a colony, he is automatically relieved and becomes part of the pool of available officers in the next round of assignments. This allows promoted officers to progress to new commands and also allows up and coming officers to compete for existing commands. Commanders in deep space will not be relieved immediately at the end of their tour but will be relieved once their ship (or squadron/division) is back at a colony. If you want to keep an officer in post indefinitely, there is a flag for this on the commander window. Planetary Governors, Sector Commanders and Task Force Commanders (and currently staff officers) are not affected by Tours.
Steve