The EP_ prefix is not needed because this is already an option of the ExternalProject_Add function. How about SOURCE_DIR_PRESERVE?
To me, the name SOURCE_DIR_PRESERVE implies that the source dir, if it exists, will not be touched by the download command or the update command at all.
If it will be modified or deleted at all, then there must be a more appropriate name than "preserve".
In my opinion, a better strategy in this case is to require source trees that need preserving or manual interventions to be setup manually and simply pointed to with SOURCE_DIR, with empty download and update commands.
My main point being: if you're actively developing code in these source trees, then they're not really "External", are they?
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