OK, now I'm in the twilight zone.
Using CWM recovery (as installed by F6Utilities2), I hit "wipe data/factory reset", and eventually rebooted it when the wipe was done.
Upon reboot, it once again did the Android is upgrading / Optimizing application <n> of 108 song and dance. And when it finally got booted, it was back to its normal self as though there had been no wipe -- SDcard hack still intact, and ALL APPS STILL INTACT.
With no re-installing, and certainly no recovery from backup, everything is still there.
I'm guessing this is because with the SD Hack, the CWM "wipe data / factory reset" is de-fanged, because it's only wiping the _normal_ data location, not the new ext4-partition-based one. Perhaps I need to also format the sdcard ext4 partition?? Or to somehow mount it under CWM before I hit "wipe data / factory reset"?
Ok, the twilight zone mystery deepens further....
My phone STILL does the "Android is Upgrading, Optimizing application n of m" thing at every startup, despite the fact that I did all of the following:
1. Reinstalled stock recovery
2. Reflashed stock 10i from the kdz file. Wiped data/cache/dalvik.
3. Left the Sdcard partitioned with fat32 and ext4 partitions, but re-formatted the partitions for a clean start.
4. Followed GameTheory's instructions to root & install CWM recovery.
5. Installed OTA Rootkeeper, then upgraded to 12b (via OTA).
6. Followed GameTheory's instructions to debloat.
7. Followed GameTheory's instructions on Link2SD.
I did not do pressy4pie's Sdcard Hack, because he seems to
now be recommending Link2SD instead -- see updates to the
opening post of this thread.
8. Installed a clean gapps.
9. Reinstalled all my apps (from Play store, NOT from backup),
using Link2SD after almost every one to prevent itne internal
storage from overflowing.
Absolutely nothing was restored from backup at any point. I would have expected this phone to now be pristine rooted/CWM'd/Links2SDed 12b. I can't immagine why it still has this quirk ("Optimizing" every time you restart it). But it does!
Subsequent cache and dalvik flushes don't help, either. Very mysterious!
(Since this problem would appear to be totally unrelated to the original Sdcard Hack, I should probably move this to a different thread. Just thought I'd mention it here first, in case anybody recognises the problem?)