Are there any drawbacks to having Cygwin and Windows share the same $HOME directory, in this case the Windows profile directory?
Merging them will work fine.
Cygwin proper doesn't store anything in your HOME directory. On first running Cygwin with a fresh home directory, default versions of
I, too, find it frequently convenient to be able to use Cygwin on things that live under your Windows profile directory. However, I don't want the two to be the same[*], so I just make a symlink to it in my home directory. I'm never farther from my Windows profile directory than a
[*] So many programs feel privileged to throw random junk in the Windows profile directory that it would annoy me to see it every time I say