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Ah, maybe I've overcomplicated things. What I was actually doing:
accessing the VM via OS's SSH Client > going to the /home/username/folder folder > executing my commands;
accessing the VM via PhpStorm's SSH Client, which was automatically going to the /mnt/UserData/home/username/folder folder automatically > executing my commands.
Now I've found the way how to teach PhpStorm to automatically go to the /home/username/folder folder and McFly is picking up the correct history automatically. So for me this isn't a problem anymore.
If you'd like, you can close this ticket now. If somebody has the same problem, then they could use that solution as well.
Use case:
/home
folder is a symlink to a/mnt/UserData/home
folder (mounted from another disk)cd /home/username
and sometimes doingcd /mnt/UserData/home/username
Suggestion:
This is good in general, but in case of symlinks I suggest tracking history based on a path where symlink resolves into.
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