lapsedgeek, before the latest stock firmware, released in May, where B&N opened up the Nooks to Google Play, the behavior you described (or something similar) may have been a problem. But it's really easy to mod the Nook now. The problem I found when approaching this was that are so many methods and options for tweaking the Nook HD/HD+ and I didn't know which was the best for my needs.
For example here are some options you have:
1) Keep the stock firmware unmodded and just use a third-party launcher.
2) Keep the stock firmware but mod it to allow the sideloading of apps.
3) Keep the stock firmware but root it to allow access to all system files
4) Replace the internal stock OS entirely with pure Jelly Bean android.
5) Keep the stock OS but put an alternate android ROM on the external SD card and boot from there (a dual-boot situation)
I am sure there are even more options out there.
I chose #2 and I'm happy with that.
If you let us know how you want to change the behavior of your Nook or what method you are most interested in, someone can point out the most relevant links where you can get the instructions.
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