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If there was a single project, the task would be easy – I could have just put it under a VCS and be done.
But I have a lot of those projects (some of which are under version control, come are not), which I want all to be in sync. For simplicity’s sake, I can say that they are all placed in a single directory, new projects are added sometimes, old ones are deleted, etc.
I’m running Ubuntu on both systems.
What is the best way to keep my work in sync?
You can use https://one.ubuntu.com/ or something else cloudy 😉 you can if you want also set up an own cloud with for example OwnCloud(you can mount to local folders http://owncloud.org/support/webdav/)
If you in the future have everything in a vcs you can push to for example github/bitbucket or your own server.