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Re: risk of virus from vmware:
No there is virtually no risk to catch a virus (pun intended). The reason I suggest for the Windows computer (what runs in vmware is practically a whole simulated computer hardware and all) to not have too broad write access to your real file system is corruption (not necessary virus only). Even though you could give vmware full access to the directory that contains your calibre library for convenience. The problem I see is the chance of the database getting corrupted by simultaneous access of the calibre in linux and the calibre in windows. Also having the epub books in your real calibre library in linux and in your virtual machine is good in case something happens to your library before you can back it up off the computer.
As for the calibre in windows (vm) or the calibre in linux concerning Kindle books - that will be up to you to decide. Make it work in linux, then you don't need to start the VM to buy Kindle books. Or make the book downloading / dedrming both in windows and only setup Alf and friends up once.
On a 12 year old computer you might get a big performance hit when running the VM, it is naturally slower compared to dual booting on same computer even.
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