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To install apps off the SD Card (sideload) you need to go into Nook Color Tools and toggle the "install apps" checkbox. Although it is checked after rooting, it needs to unchecked and then checked to really work right. After that you should be able to install .apk's from gmail, sdcard, dropbox, amazon, etc.
The whole file system won't be visible when using the usb cable. You can download file explorers on the Nook to work with the file system. Astro is great free one. Root explorer will let you see/modify the entire filesystem. CAREFUL!!!!
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