Should I aim to create different CPAN work directories?
No ... though you can if you want to.
I have multiple perl installations with different configurations and version numbers, and they all use ~/me/.cpan as their CPAN build directory.
It has never been an issue on Linux for me.
On Windows, it's the same situation - though I did have to make a small hack to .cpan/CPAN/MyConfig.pm.
Because some of the windows perls use different flavours of "make" I had to change 'make' => q[make] to 'make' => $Config{make} (which, IIRC, meant that I also had to insert use Config; into MyConfig.pm).
Cheers, Rob
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