If I want to cook natural farm eggs with its shell at low temperature (65C-150F) for 20-30mins and they have some dirt at shell is better to clean it or not? If it's better to clean it what's the better way?
When raising eggs, rules for cleaning eggs for sale varies drastically by jurisdiction. In the US for instance, the USDA issues guides, but actual rules are set by each state and many have rules drastically different than the USDA rules. Some for instance do not allow the eggs to touch water at all, while others require it. Having been licensed in two states, and researched it for other, I will avoid some of the contradictory reasoning used by different jurisdictions, and you are interested in your own usage in any case.
Rules for cleaning are largely concerned with storage, not immediate usage. When an egg is laid, it gets a layer on the shell called a bloom. Provided the hen is healthy which is part of the goal of getting farm fresh eggs and using the assumption that the small farmer is taking good care of their birds, the bloom contains natural bacteria fighting effects on the shell and is desirable to leave in place. As soon as the egg is washed, the bloom is removed and this minor protection is lost. Any egg that would be classed as nest clean should generally not be washed for storage to be classed as farm fresh. A nest clean egg should little of no manure, and minimal dirty. Sometimes they do, but the majority of the eggs should not. If dirty, they should be cleaned before sale and used much more promptly. 30 days from harvest for an unwashed farm eggs should still be as fresh as any egg from the store, while washed, I would personally use within 2 weeks if possible. If more than a couple eggs in a dozen though are dirty, I would consider if that was the correct source for me, the nesting area may not be kept clean enough at least for my use.
Now, for you personal use, yes clean them before use, but preferable is clean them just before use, or at least not long in advance. When cleaning, you want to water to be at least 95F degree and no more than about 105F (35-40C), about body temp and warmer than the egg. Cool water will cool the egg and create a negative pressure which can draw water, and with it contaminants through the porous shell, while warmer with create a positive pressure and keep the water out. Avoid scrubbing as you may push contaminants in, rather, brushing clean. Most recommendations for raising so never soak, and even for home use this is a good guide in most views as well because again, the shell is porous and soaking will allow water through. In general, again, if the eggs is dirty enough to require soaking or scrubbing, well, you are getting eggs that may not be the quality you are looking for by getting farm fresh instead of factory.
In general, farm fresh it is hopeful you are reducing your risk of things like salmonella contamination, but if you eggs are not nest clean, that does not really give a lot of confidence you are getting what you are after.