When Meanie upgrades the fixed pdaXii13 Akita I will give it another go, but is what you propose possible Jon_J? I know under Cacko it asks you where you'd like to install an app but afaik the pdaXrom package manager doesn't give you the option of instaling to NAND or MD but I'm sure you could probably manually move and link the files after installation although that could be quite tedious.
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I partitioned my microdrive to the default setup awhile back when I installed pdaxii13 (5.2) to my hard drive (I installed pdaxrom beta3 first)
I then reformated my hard drive (hdc1) I reinstalled pdaxrom beta 3
Later, I installed pdaxii13-akita, which overwrote pdaxrom beta3
Now I installed pdaxii13 full image to my hard drive hdc1
Here's a screenie of package manager with the available mounts to install software.
EDIT: Yes you can see in the screenie that there are things installed twice. (double vision)
Those double entries are showing pdaxii13 full image on the hard drive (these don't actually have desktop counterparts)
The double entries don't actually effect anything, since my hdc1 partition is manually mounted and isn't linked anywhere.
The other half of the double entries are the programs/libs, etc that are on flash. These are the actual working ones.
I'm just waiting for meanie to update the full upgrade, then I'll either uninstall the duplicates, or wipe everything, and start fresh again.
The duplicate install does come in handy for copying .desktop files for when I install something new to Flash and it doesn't "register", and if it does have a .desktop file in the duplicates.