I know this thread has become more about technique than why..but my mod is on that list and yea I guess it's true my mod hasn't been cleaned(never heard of it until now). It's several yrs old now and I just haven't ran across any problems with it not being 'clean' ...and according to the list most items Bethesda release aren't clean. That's the standard I would use as far as necessary steps. I have painstakingly avoided dirty edits and looking at TES4 edit my records reflect my carefullness. Cleaning IMO is nice but more for mod hobbysts(those who collect tons of mods) than the typical player. I never run more than 40 mods at a time. I'm not sure whether to feel somewhat offended or indifferent towards mine being on a list that could possibly carry some kind of negative implication in the community, nobody ever notified me. I guess I'll just leave it at that and see if 'cleaning' brings any benefits for my plugin performance.
edit: Did a quick run and the cleaning process removed 53 records..most of which I knew exactly what they were and intentional (some shifted trees and rocks). *shrug*.
I've never seen this list so don't know how things are worded, but I would hope that any such list would have been presented carefully so as to try to avoid any negative implication towards the mods listed. Most mods do not NEED cleaning. Only a tiny minority really NEED it. All mods would benefit from it, and the more mods a player uses, the more important it is for them to be using cleaned ESMs and ESPs, so as to reduce conflicts which could negate certain changes made in one mod by a later loading mod that accidentally contains edits to the same objects.
BTW if 53 records were removed, then these are not the ones you are thinking about with regards intentional edits. Auto-cleaning (which is what you did there) only removes records which are identical to the last-loaded preceding ESM or ESP containing the same record (almost always just Oblivion.esm for most mods). Being identical to the previous-loaded ESM or ESP containing that same record, they will not have been shifted by any amount, not even 0.001 of a point on the x, y or z coordinates. The trees and rocks you are thinking about which you had shifted are NOT amongst the 53 records removed, they are still in your ESP, shifted to wherever you shifted them. These 53 records were not intentionally edited by yourself when working on the mod. Either the CS just slipped them in (it loves doing this. I think it gets some sick pleasure from trying to see just how much undesirable data it can slip into an ESP without the modder noticing), or these are records you looked at the properties to, then clicked OK instead of Cancel without changing anything. Clicking OK will tell the CS that the record is updated (even when unchanged) and thus add it into the ESP when you save. Similarly, anything you accidentally clicked and dragged, then clicked Undo or pressed Ctrl+Z to undo the move, will still be seen by the CS as updated, even though you moved it back by undoing the edit. Again such records will get stored in the ESP when saved.
These are all annoying little quirks of the CS, and nothing that the modder has done wrong. Without a tool like TES4Edit, no one would likely even know it had happened, and most of the time, they're harmless. But, sometimes, someone will be using another mod which happens to touch on the same part of the game. And this is when these unintentional edits show up.
It's not the mod-creator's fault; they shouldn't be blamed, or accused, they shouldn't be pestered by people because of it. There is nothing wrong with the mods (with a tiny minority of exceptions), but a polite mention (if a serious issue has arisen because of these unintentional edits) is reasonable if the modder is still actively modding. The wise move would be to politely mention this via PM, rather than in a thread on any forum - some modders might get overly defensive if you post in public where all can see, but might be more accepting if the topic is brought up privately. If they're not interested, that should be the end of the topic.
Okay, so now we are back to cleaning ESMs. This is like banging my head into a wall...Okay, so the same rule applies. Clean the dependencies first. Definitely do not hide them while cleaning. I need to go do a slight update then...Oh, for those of you who are new to this, what Psymon did is exactly why newer mod users should NOT clean random mods. You should have the knowledge to anolyze the changes done by TES4Edit, in the case of duplicates. I say undeleting deleted references is good for just about anyone. If the mod is currently being worked on, let the authors know, just be polite about it.
Edit: It still stands that some duplicates are intentional. I still think FCOM should be left alone. WarCry seems to be okay to clean, but Corepc said the files get covered up by the rest of FCOM anyway. I cleaned it... I am a little unclear on those Fran duplicates. They should be left there? Is someone working on Fran?
Yes, you should always clean from top to bottom of the load order when ESPs are dependent on other ESMs or ESPs (but only if you know what you're doing with regards ESPs dependent on ESPs!)
Start with the ESM, then the ESPs dependent on the ESM. It is rare (in my experience) for a mod to come with an ESM needing cleaning - most mods which use ESMs were created by modders who know the limits of ESMs and created their ESM avoiding doing things likely to create duplicate records in their ESM.
Some identical-to-master duplicates are indeed intentional. However, this can ONLY ever be true when the mod containing these intentional identical-to-master records is explicitly or implicitly dependent on another ESP. If a mod which is not explicitly or implicitly dependent on another ESP contains identical-to-master records and they are claimed to be intentional, they're not. There is NO good reason for a mod which is only dependent on Oblivion.esm to contain records from Oblivion.esm which are identical to their existence in Oblivion.esm. The only reason I can think of for intentional identical-to-master records in a mod only dependent on Oblivion.esm, would be to try force potential conflicts with other mods as far away from intentional edits as possible, in hopes that when someone comes across a conflict caused by this, they won't link it to the mod which caused it, as that mod's intentional edits aren't nearby (such as duplicating LAND records in a full 3x3 cell radius, where your mod only actually edits the centre cell - the other eight cells around that one cell will push any possible land tears to the outer edges of those eight cells, nowhere near the one cell your mod intentionally edits). This would not be a valid reason to contain the LAND records from those eight cells.