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5% of the time, there are internet jitters that make this not feasible and I rsync the directory and continue working locally. Sometimes after this I'll end up working again in the repo on the server and so end up with two directories that started at a common point but have diverged.This is not the way to do it. Ideally, you'd git push whatever branch you're working on on the remote server, then git pull on your local workstation. Not rsync. This is a workflow problem, not a tool problem. I knew someone who would copy files from a repo to a temporary directory and work there. That is just not the way to do it.
>Ideally I want to do a kind of 'rsync merge'
I think you want to use git correctly at first and see if the limitations still persist (they won't, they almost never do).
>I don't want to temporarily create separate parent git repos since the directories themselves already are git repos and that sounds like a confusing recipe for disaster.
>Is there any kind of standalone 'git merge'-esque tooling for independent directory trees?
The above is the recipe for disaster. Please consider giving `git` a shot. I work from a location with internet bandwidths at the kbps levels (not kilobytes, kilobits) levels, power outages, and telcos randomly assigning you phone numbers of other people. This is one reason that drove us to create our machine learning (ML) platform in the first place (because we needed to launch ML training jobs that consumed data of data and we simply could not be downloading and we considered at some point having someone fly with a disk with 60 GB of data - not terabyte, just gigabytes, to tell you how much it sucked-). We also had users with 5 kbps (again, five kilobits per second, not five kilobytes per second) connections so I'm more intimately familiar with this issue than I'd ever want to be.
