The reason is that we put some new functionality in the Modules area to make it easier to work with when the idea is being developed or tried out. Eventually it gets merged into the core files and and removed from the Modules area. IE the folder or file(s) get deleted. In this particular case the functionality had 3 parts; one has been moved into core, one has been left in the Modules area as it provides a temporary fix for a problem we want to address another way, and the third bit was removed because it did not do anything.
Most changes in Caveman2Cosmos wont break saves. A lot of work has been done to make saves robust enough to handle the more common changes that would break saves otherwise. You will get one off in game messages saying that something has been removed or changed but XML errors you should not get.
When a new version is made delete the old code (folder) and create a new with the release.
If you are using the SVN it will delete as well as add and update files and folders, you just need to be sure that if you are not using the SVN copy as your game copy that you synchronize you game copy fully.
We did break savegame compatibility from 38.1 to 38.5. You'll need to completely erase the old mod folder and put the new mod folder in place thereafter. The old save will not continue to function but the good news is it should be a much better game from here.
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