Also, just some questions on the native reader application:
When I go to settings, to turn on animated page turns, the reader crashes (it often crashes and it doesn't feel stable in use). Also, the reader by default displays a PDF full screen but when turning to landscape and back to portrait it takes a large strip from the top and bottom off and renders it black and so shrinking the reading area. Overall the native reader app seems buggy to me and was wondering if there is a solution or something can be done to get a more stable experience using it?
I believe the Calibre program (runs on a Windows box) can convert unsecured PDFs into ePub (and maybe other formats). You can then copy the file to the Nook.
Amazon probably offers the mentioned service since the use a proprietary file format on their readers and needed a way to allow the many free ePub/PDF sources to be usable.
No idea on annotations. Standard Android programming (at least from the books I've read) is that 1) each application gets its own private data store (yes, the data belongs to the application and not the user) and is not shared among applications (the library app can start the reader app passing the path to the book, but the reader app has no access to the library list); 2) applications should use SQLite3 to store persistant data.
You really don't want a PDF converted to an EPUB, especially one done with an automatic tool. PDF's have so much baggage that it makes the outcoming file rather difficult to read. If at all possible I would try to get your documents in a reflowable format (.txt or .docx or such) and convert those to EPUB.
1) Clippings File - I've never seen any mention of anyone accessing this. I think it might not be possible. As Wulfraed said, each app in Android has its own private space and that isn't accessible unless you root.
I remember trying with the Nook Color to locate the highlight files and couldn't really. Of course, I only tried fleetingly.
1b) Does EZPDF not offer this? To export clippings from PDFs?
2) There's no 'Send to Nook' feature, to th ebest of my knowledge. Your options are to use Dropbox (to save file to your Dropbox folder on your PC, then have them on Nook Dropbox App), to use INstapaper (available on nook), or use something like Pocket or Drop It Later (not sure if this is available).
2b) Another option is to save files and transfer wirelessly to Nook using Open File Explorer App. However, they have to be on same network.
2c) Nook browser has an Article Mode. So you could use a bookmark site like Delicious or Stumble Upon to mark articles. Then later log on via HD+ browser and use Article Mode.
3) Stock REader does have some issues. B&N has been slowly (but steadily) fixing issues in HD and HD+. I suspect they will make the reader more stable over the next few months.
It helps to restart your Nook and to make sure you don't have apps running in the background taking up memory. Try App Killer app to see if any unneeded apps are running.
Restart Nook -
Power Off: PRess and Hold power button for 20 seconds.
Power On: Press and Hold power button for 4 seconds.
3b) If you save files to your Nook (as opposed to SD Card) that also helps in making things more stable.