Hi David! Running Windows programs from the "Windows side" via Wine is
frowned upon and can break things. Sure, ever since NTFS there's the issue
with not having full support for that filesystem in Linux or Mac, but
there's the big issue of programs not syncing back to Windows's registry
because they (nowadays) only read and write to Wine's registry. In fact,
they don't even see the windows side as the C drive, so a lot of things can
break.
I didn't know that once upon a time Wine could use the real Windows
registry. That's interesting.
Well, you can try importing registry keys over. The Wine registry editor accepts
*.reg files. And you can make multiple prefixes at will, so you can at any time
create a fresh prefix for experimentation, and delete the prefix if something
doesn't work.
There's lots of tools that can help you. From your Windows side, you can run
the Magical Jelly Bean Keyfinder to extract a lot of keys that you can use to
reinstall your programs on your non-Windows+Wine side. The Magical Jelly Bean
Keyfinder can not yet load a hive (binary registry file) from within Wine.
I do know that you can view your Windows registry from Wine using the MiTeC
registry viewer (at least last time I tried it worked). It might even be able to
extract *.reg files for you from your Windows registry which you can then import
into an experimental prefix's registry using Wine's registry editor.
If that fails, you can boot back and forth as you extract stuff to *.reg files
with Window's registry editor.
If you really wanted to be adventurous, you could try importing your entire
Windows registry into an experimental Wine prefix, and then copy files from your
Windows side into the prefix, but that sounds bound to break something.
You can also use virtual machines to get a fresh installation of Windows, then
using WhatChanged and RegShot, you can take snapshots before and after
installing programs and activating programs. Then you specifically know what to
copy over to Wine.
Cheers,
Jake