I would like to add an official response that this is completely wrong, both technically and content-wise.
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=== THIS IS NOT RECOMMENDED BOTH BY OPENXCOM DEVELOPERS AND BY XCOMFILES MODDER ===
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1/ First of all, the standard xcom1 mods are NOT COMPATIBLE with XcomFiles and the modder consciously decided to change the mod distribution, so that you CANNOT activate them. In best case, you get undesired results (like the improved base mod you showed for example... which makes the game basically unplayable because it removes required facilities like Xcom Headquarters, etc.)
2/ Second of all, the method of the mod installation you showed is also completely wrong. XcomFiles supports normal modding just like UFO (or TFTD or PirateZ, etc.). Each (sub-)mod should be in a separate folder (under "/user/mods/" if you're using portable installation) and activated/deactivated via GUI. You should not change anything directly within the "XcomFiles" folder.
@all: please do not do this (or suffer the consequences)