The mod ruleset only overwrites what's in it, all the rest is taken from the Xcom1Ruleset (and any other enabled rulesets, in priority order). So these mission weights are just added to the already existing ones. The way to disable mission/race is either setting the weight to 0 or using the delete command (but some missions/races are still hardcoded to appear, disabling research, terror, retal, infiltration, alien base or alien base supply is probably going to cause trouble). The only things that aren't checked piecemail are lists (stuff that starts with -, like in Alien Origins research topic); redefining a list replaces the whole list.
Example: to change the cost of a pistol, you just need to write:
items:
- type: STR_PISTOL
costBuy: 5500
all the other, mising info on the pistol will be taken from the base ruleset.
and delete command:
research:
- delete: STR_LASER_WEAPONS
Always check what your new stuff takes from the base ruleset/other mods! Else you're in for nasty surprises
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