[Android Software/Hacking General [Developers Only]] Quantumstate:
I've tried and tried to get a number of questions answered here and on the Cyanogenmod forum, but either my questions are extremely advanced and esoteric, or everyone here is just users and developers are somewhere else.

So I'm creating this thread of Mysteries To Science, for all those questions you have which no one is able to answer. I've run Debian exclusively for 14 years and am used to having total control, and the lack of knowledge on Android here is perplexing. I have the Nexus One, but I think these questions apply to essentially all Android phones.

Here are my Mysteries:

Messaging Problem - I use ChompSMS. A couple weeks ago I stopped receiving text messages, about the time I removed the stock Messaging app using Titanium. I can send just fine, but I never receive them.

Anyone seen this problem? Does Chomp use its own system, or does it depend on Messaging? I reinstalled GApps thinking Messaging is there, but it's not. Is it a dependency, and if so where is it? If not, why do I no longer receive and what can I do about it?

App Shortcuts - I created a desktop direct messaging shortcut to call my boss, with a pic of an angry boxer dog. Made the pic as a gif and png with transparent background, although it is ending up as black on the desktop for some reason.

I assigned the pic as the shortcut's icon using Gallery, and I suspect that Gallery is converting the background to black, but I cannot find where app pics are stored either on the SD or /system.

App Sorting - Also like so many others, I have many many apps. I have always categorized my apps, since I started using Debian exclusively 14 years ago. To have all my apps dumped into a giant pile as they are in the N1, is irritating. I installed Apps Organizer, but it seems to want me to tag each app with a category, rather than basically making folders with categories such as Utilities, System, Multimedia, etc.

Is there any way to make folders for the apps?

Calendars - I am not sharing my personal information with That-Search-Engine-Everyone-Uses. (Yes, I've deinstalled all GApps except Market, and use exclusively AppBrain's app to install apps, but still haven't found a way to buy apps in a way I trust) Can anyone recommend a calendar app which is compatible with Linux and M$ calendars, yet doesn't sync with some Outside Authority?

Compass - The magnetometer in this phone is completely unreliable in my experience. Any stray magnetic field throws it off by 18 degrees permanently. The only way I've found to almost calibrate it is with the Compass app Calibrate function, but to run that before any other app which requires a compass is a headache. Is there something I'm doing wrong?

SD Card - What relation does the SD card have to the system? Why is it that when I install an app to the SD card, its widget is no longer available and its daemon will not run? Is there some way to add the SD card to the kernel's awareness for these purposes?

Factory Reset - If I back up system and apps using Titanium, and desktop and ADW settings using ADW, and export contacts, is that enough?

What are the data structures in Android? I know there's the kernel, and ADW is the full user interface, but where are contacts stored? Where are apps, /system/apps?, and if so where are their config files? Where are the desktops configured, and where are the shortcuts+icons stored? I can't find any such config files, and the only one I know of is the central system config file /system/build.prop.

How to recover my contacts? Apps installed in phone memory? Would a restore, restore whatever is ostensibly messing up the compass?

So given wherever these data structures are, what effect does a factory reset have? Exactly which data structures does it wipe/replace?