Read This - Re: Jailbreaks, Categories & awesome effortless way to restore
Sorry for the lengthy post...
LOTS OF GOOD STUFF I promise!
I also love Categories, but the problems described above can be a 'forced consequence' of having Cat. installed with Inst. & Cydia hidden in folders.
As others said above, unless you delete Cydia/Inst. from Cat. folders you will be 'locked out' of these progs unless you follow the simple procedure below...
1-) If you re-jailbreak right after the firmware restore (meaning before you use your iTunes' iPhone backup to restore settings, etc.) you WILL see Cydia/Installer. They WILL disappear once you restore your iPhone settings, but that's where the 'workaround' comes in.
2-) Immediately after the JB is performed you launch Cydia and install a pkg called QuickGold. This prog. launches when you push the home button once, while on SpringBoard, and it brings up a pretty cool launcher/search engine.
3-) After installing this, go ahead and restore your iTunes iPhone backup. When done you will see that Cydia and Installer are gone.
4-) Push the home button, again while on SpringBoard and 'like magic' Quickgold launches. Type 'Cydia' in the search bar and the icon for Cydia will come up on the list of items that match your search.
5-) Launch Cydia, then install BossPrefs. If you had BP before and had it hidden, it too can be launched from QG.
6-) In BP tap on "Poof" at the bottom, and a msg will appear saying it is "enumerating apps..."
7-) When that's done, it will list ALL apps installed on your phone with a little on/off switch. Cydia, Installer, etc. will appear to be 'off.' Simply turn them on, and DONE DEAL! Press the home button once to exit. SpringBoard will relaunch and 'VOILLA' ALL your apps are back. PROBLEM SOLVED!
Quick Gold has 'recents' in it too, so if there's an app you use a lot (yes even appstore apps) just look it up from QuickGold one time and a shortcut gets added to QuickGold so that next time you launch into it the app shortcut is there (as opposed to flicking through several screens to try to find your app or if you use 'Categories' having to wait for the folders to launch, etc.
More about restores...
I used to hate having to restore my phone (heavy Cydia user)
I used to lose all my themes and other apps and would have to start reinstalling everything from scratch (3+hrs.) until I discovered a package in Cydia called APTBackup... this is an AWESOME app as it creates a backup text file that backs up to itunes when you backup/sync. All you have to do is launch the app and hit the 'backup' button.
Once you have created a 'backup of your backup;' (backed up your Cydia backup to iTunes) you restore then you re-jailbreak and THEN you restore your iTunes backup.
Finally, you launch Cydia and all you install is APTBackup.
Because your itunes backup contains the APTBackup data, you are able to hit the 'restore' button within the APTBackup app and like magic (it will take several minutes though ) all your Cydia apps, themes and other installs will restore/reinstall themselves without you having to manually reinstall/configure ANYTHING!
As for AppStore Apps you will have to re-sync to reinstall them to your phone as the iTunes back-up no longer backs them up. (I will take that 100 times over waiting 1hr + for backups to both be made as well as be restored after a 'restore.')
Lastly, if you do use Categories, you WILL have to re-create the folders, put the apps away, etc.
Hope this helps!
