[4.2 LTS, 4.3] My Blender projects are typically in a cloud folder, where I really want them. By default, physics (i.e. fluid) caches are created in a sub-folder of the project. This causes quite undesirable cloud behavior.
I can relocate the caches to a better location (tedious manual process), once they have been created. I haven't seen a way to prevent the situation. "Preferences > File Paths" doesn't seem to offer help - I tried several items.
It would really be nice if there were a preference setting. Maybe there is something I've missed?
Hey, I've been annoyed by this as well especially when using synched drives. your question triggered me to finally go look for a solution :). I think (and it seems to work for fluid sim) you can choose a folder for your render cache in your preference and your bakes/physics will also go to that folder . 
Thanks a lot slenaerts - it seems to work (sometimes). I had already tried this once, but I guess I hadn't scrubbed the timeline to create the cache yet, so I didn't see anything.
The first time I create a domain, it seems to work. [If I copy the domain, the second one has the same cache as the first.] If I delete Physics:Fluid:Domain and add it back, it seems to revert to the old behavior (subfolder)...
