Will those "mined resource items" be in your storage/terminal and counted at season ending or will it be more like the power processing? If you keep the resources in storage/terminal it'll be more exiting near the end of the round since they can get stolen by aggressive other players.
Bug reports, critical problems in the game or site not related to your own code
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I have the same issue.
I installed screeps yesterday, the scripts are trivial and genuinely don't do anything that isn't covered by the tutorials. I do also edit them in an external editor, but I doubt it's related.
Last night I turned off the private server, then restarted it this morning and all spawns are at 0/0 energy (mine and those that belong to the default bots.)
Can remove them with the CLI. default steam I think its removeWhere. Mongo just remove, so depends on what your using. Could also use mods/make a mod to disable them.
I'd recommend joining slack and asking around #servers, slack tends to be quicker/livelier responses.