I want to keep the above setup, the remote branch that will track my local will be on 

fork

 so it needs to pull from there. Currently it recognizes 

origin

 so it doesn’t work because the agent then can’t find the commit.

So you do not want to push the change set ?
You can basically add the entire change set (uncomitted changes) from the last pushed commit).
In your clearml.conf, set store_code_diff_from_remote: true
https://github.com/allegroai/clearml/blob/8708967a5ef4d8529a1a5ea417672e3ebbb258d7/docs/clearml.conf#L157

Will that solve the issue ?
(obviously you can manually change the commit/repo after you call execute_remotely, but I'm trying to find a solution that avoids that)