Search for and download both OpenSSH, MobileTerminal and Afc2add onto your device.
Method 1:
1) Download iFunBox, either the new iFunBox 2014, or the old 2013 one, either will work
2) If you downloaded 2014, run iFunBox Classic. If you downloaded the 2013, run iFunBox, then on click on "iFunBox Classic" on the top left.
3) Plug your device in, and wait for iFunBox to recognize your device
4) Expand the directory tree for your device and click on Raw System File
5) Navigate your way to /etc/apt/sources.list.d/ and make a copy of cydia.list onto your desktop, then edit it using a word processor, preferably NotePad, NotePad++, plist Editor or any other simple text/scripting utility.
6) Check to see if you see the line "deb
Index of / ios/847.21 main" where there's a space between deb and http, a space between .com/ and ios, and a space between 847.21 and main. If not, edit/add it in the exact same format.
7) Save the changes you've made. If there was no need to change/edit/modify that line, proceed to method 2. If there was a need to edit the source list, make sure you copy the changes back onto your device by dragging and dropping it back into the proper directory where you found it.
Method 2:
1) Run MobileTerminal on your device directly.
2) Type in the command "apt-get remove cydia" without the quotes.
3) Let the command finish, it's thing, then close out.
4) Download iFunBox, either the new iFunBox 2014, or the old 2013 one, either will work (do not have to repeat if you used method 1)
5) If you downloaded 2014, run iFunBox Classic. If you downloaded the 2013, run iFunBox, then on click on "iFunBox Classic" on the top left.
6) Plug your device in, and wait for iFunBox to recognize your device
7) Expand the directory tree for your device.
8) Scroll down the directory tree until you see Cydia Auto Install
9) Download, then drag-and-drop
this file into Cydia Auto Install.
10) Reboot your device
11) Run Cydia and let it finish the initial setup
12) Re-launch Cydia after the the initial setup closes our Cydia. Let the sources re-cache. There should be no issues. Cydia will now prompt you with essential upgrades. Tap on temporarily ignore, then tap on Changes at the bottom. Make sure Cydia Installer is on the list of upgrades available, then tap on the top right to upgrade everything.
13) Your device will either need a reboot or a respring afterwards.
14) Once your device has been rebooted/resprung, open up Cydia again and you should have gone from Cydia 1.1.8 to 1.1.9, and you should no longer have the Cydia source issues.
Method 3:
Since all hell broke loose, navigate back to /etc/apt/sources.list.d/ and replace the cydia.list you have on your device with
this one. It's not a clean source list, but it does include several sources that can be of use for betas and such.
Let me know if any of them works. I haven't encountered the issue yet so I can't personally test it out, but they're all safe-to-do steps.