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Job executors are modeled as list of serializable objects in OneDev, and a single executor does not have id for update/delete. So they are getting updated as a whole. It should not impose any performance problems or conflicts as long as you are the only one to update.
As to project level executor/agent, I filed a feature request OD-2131. Due to the added complexity, that might be a EE feature in future.
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By now the onedev server (v11.3.2) provides the only "Set Job Executors" ( POST /settings/job-executors" ) RESTfull API for me to manage all my job executors. This is bad when I got hudreds of job executors to manage. The reason why I got so many job executors is because we have hundres of exclusive agents for each user (not sharing agent resources between users). I think the easiest way to solve this is to add 3 create/update/delete job executor RESTfull APIs. Or can you make job executor select agent dynamicly at job runtime?
And by the way, would you guys provide project level job executors please? (Maybe this is bad idea)