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Troubleshooting Cydia: Problems with Broken Repos

I had a scary experience last night. As I was searching for a certain tweak in Cydia, I noticed that I wasn’t getting the results I was looking for. So I searched for a few more apps and tweaks, and I kept getting no results. I thought about it for a minute, and then realized that every item I had searched for was from the BigBoss repo.
I’ve recently upgraded to the iOS 4.3.1 jailbreak, and I haven’t gotten to play around with my main iPhone setup that much yet.
To my surprise, the BigBoss repo was broken in Cydia. BigBoss is a pre-installed repo in Cydia, so it’s very odd that it wasn’t working. The good news is that there’s a way to re-add default Cydia repos without re-jailbreaking the iPhone…
The Telesphoreo Tangelo (saurik), ModMyi, BigBoss and ZodTTD repos come pre-installed with Cydia when you jailbreak. Unlike repos that you manually add to access more content, these default repos follow a different APT structure. Because these repositories have different branches, source builds, user permissions, etc, it’s impossible to simply delete and re-add them in Cydia like you would any other repo.
If one of these key repos is corrupted in your version of Cydia, you lack access to a large percentage of the content that’s indexed for the jailbreak community. And that’s a sad thing.
If one of the four main repos is broken in your version of Cydia, chances are that something went wrong when you jailbroke your iPhone, or you messed something up through SSH.
A good way to generally tell if a repo link is broken is to check its icon.
When you look at your list of repos in Manage > Sources, you should see either a specific icon for each repo or a question mark. The question mark usually indicates that a repo is either corrupted or empty.
You can tap on each repo in your sources list to see the content that’s being delivered for that repo, and a broken repo will have no content to display.
If one of the four pre-installed repos is indeed broken, you can’t re-add it like any normal repo. You have to tunnel into your iPhone’s file structure through your favorite desktop SSH client. (I recommend iPhone Explorer.)

Step 1: Navigate to root > private > etc > apt > sources.list.d

Step 2: Add the .list file for the repo you want to replace.
If you want to make your own .list file, open up TextEdit (Mac OS X) or Notepad (Windows) and copy the following text:
# do not edit this file to add your own custom sources
# this file is subject to be upgraded as part of a package
# either add your own .list file to /etc/apt/sources.list.d
# or add your entry to the global /etc/apt/sources.list file
deb http://apt.thebigboss.org/repofiles/cydia/ stable main
(Replace the URL with the repo URL you need to fix.)

Step 3: Save the file as a .list to your desktop.
Example: “bigboss.list”

Step 4: Add the new .list file to the sources.list.d folder.
Make sure there are not any existing copies of the file you are adding. If the desired .listfile already existed before you added your new version, make sure to delete it.

Step 5: Respring your iPhone!
Check your sources in Cydia to see if your repo(s) work again. If not, you can try adding the ModMyi or BigBoss repo under the Telesphoreo Tangelo source list.
While this method I’ve highlighted has proven successful in multiple instances, it isn’t fail-proof. Always have your data backup handy in case you need to restore your jailbreak.
Let us know about your Cydia repo woes in the comments below. Did this method help solve your problem?