Here is a quick guide what you can do (mainly using SSH to access files on your iDevice) in order to cleanup Cydia Settings / Cydias Repositories. This guide applies to the recently published Cydia 1.1+.This guide is based on the excellent Quick Guide at modmyi.com...Word of Warning:

• Remember not to delete any directories! Just delete the files mentioned below. If you delete directories Cydia will fail to open.
• Write down your custom repositories. It is always good to have a backup of your precious repository links. Cydia will re-initialize (ask you again: are you a user, hacker....) so you may need to enter information about your custom repositories.
• As an alternative to the below method you can use iFile directly on your iDevice.

Prerequisite - SSH into your jailbroken device:

• Make sure OpenSSH is installed on your iDevice.
  • On your iDevice open Cydia.
  • Select "Sections" in the Navigation bar at the bottom.
  • Select "Networking" from the list of sections.
  • Select "OpenSSH" from the list of packages.
  • Press the install button at the top right of the screen.
  • Press the confirm button at the top right of the screen.
  • Once the install completes successfully press the return to Cydia button at the bottom.
  • Hit the home button (physical button) to return to your home screen

• Activate WiFi and get your IP-Address.
  • On your iDevice open "Settings"
  • Press Wi-Fi at the top of the settings list
  • Chose your Network and follow the on screen instructions
  • If you are logged into your Wi-Fi network continue below:
  • make sure you are in: Settings > Wi-Fi
  • Next to your network: press the circular blue arrow button
  • In the information section below the buttons you will see "Ip Address ...."
  • note down the IP Address

• Log into your iphone using a SSH client on your Mac or PC
  • Download and install a SSH client on your mac or pc.
  • If you do not know how to do it.. Search for Cyberduck and guide...
  • Open a new connection
  • For server or hostname enter: <the IP Address you noted down from the previous block>
  • For user name / login enter: root
  • For password enter: alpine
  • Click login or connect etc.
  • After you confirmed any potential key warning you should be connected to your iPhone

Reset Cydia - Delete your Repo Settings

• Navigate to: /var/lib/apt/lists/
• There: delete all files (do not delete directories, especially do not delete 'partial')
• Navigate to: /var/lib/cydia/
• There: delete metadata.plist
• Navigate to: /etc/apt/sources.list.d/
• There: delete all files including cydia.list
• Exit and disconnect | then restart your iPhone (or respring)

Now when you open Cydia again everything should work fine.