Android File System Structure?!

[[sammich]]

Coming from Windows Mobile, I knew I was in for a bit of a shock. But I didn't realize it would be this bad.

You see, I have OCD when it comes to organization and cleanliness. It's pretty bad. On windows mobile, I had every program organized by category. I edited all the .cab files to install to "\Program Files\*CATEGORY*\App Name", and the shortcut to be installed to "\Start Menu\*CATEGORY*"

Everything was perfectly organized. On the root of my SD card, I had 2 folders - "My Documents" and "Program Files". There were no stray files on the root.

I had everything setup PERFECTLY with Sashimi so when I reflashed, I could run my script and all settings/apps would be restored.

I found the registry key for all settings and backed them up, made provisioning XMLs for all of my account settings, etc. Anything that needed to be saved between flashes would be saved to the SD card. When I flashed, everything would be back to the way it was an hour ago.

I LOVE my Evo 3D, but I'm getting incredibly frustrated with how insane the clutter is. Every app and its mother decides to make a folder on the root of my SD card. And half the time, they're empty folders. I just want to know:

1. How are settings stored in Android? In WM, there were registry keys for everything from backlight to email signatures. Where and how does Android store these settings?

2. How can I have an app completely installed on the SD card, so that if I hard-reset, all I need to do is put it's shortcut in the app drawer?

3. Are there any tools like Sashimi that streamline the hard-rest/reflash process?

Thanks in advance