Oh huh, that's a big step. and certaily you should open a new thread to dicuss that. or better a thread for each departament.
Ok, looking through the link i like your classification. but: there too many departaments IMHO and way too many civics and configutations to choose from making each less special. i think that the departaments of executive, legislative, juristicion, religion, defense and economy are fundamental while the rest seem to go too deep into detail and should partially be merged into other categories. but one category that i miss is the social structure of your empires society (communism should be in this category since it a social model together with caste, slavery or surveillance society). maybe call it departament of social affairs.
let's go into some detail about some of 'minor' departaments:
1. agriculture: the policy in this sector is mostly dependant on the society model and the economy you run. therefore i don't think we need a distinct departament for this.
2. commerce: i'd call it economy departament.
3. energy: public & private? this rather belongs into economy.
4. homeland security: sounds strage, at least for not US citizens. ok but you think of it as a 'secret service' departament which is indeed not covered by the other groups. i don't think we need this as long as there aren't more factors its civics can influence (like increase cost for enemy esionage, spy stating xp, detection probability...)
5. housing: it's covered by economy, society and executive.
6. labour: from what i see in your list it's what i'd understand under the term social model.
7. immigration: well it could be intergrated into another catagory (slavery is based on slave immigration i think) but it could be discussed as an own group for the later epoches.
8. waste: better named 'departament of ecology'. parts of it this could be merged into economy but i think it's worth an own departament when it's competence would cover more than waste.
9. health: a proplematic topic for me. it's hard to talk about the health system of the ancient greeks. and untill now
and
weren't that relevant in RoM. so maybe wait with this until AND balaces health that it becomes an issue.
10. i see that a lot of your civics deal about how your empire interacts with others - not only on economic level. therefore one could take a departament for foreign affairs/policy into consideration that explicitly handles such issues.
11. in executiv departament: communism isn't a goverment but a society model. if you think of the soviet union it's dictatorship. or when you think of what it should be ideally it's 'council republic' or soviet republiic ('soviet' rus. = council) which is one of the most democratic system ever know.