iOS hacker and developer Jay Freeman aka saurik has pushed out two updates back-to-back for the Cydia Installer, which are version 1.1.25 and 1.1.26 respectively. The version 1.1.25 moves all your jailbreak content to the user partition from system partition.
You might have noticed that the "Preparing Filesystem", after installing Cydia Installer 1.1.25, works faster. This is because Cydia did not move the jailbreak content to user partition . saurik says this update will minimise the issue some users were facing with a "late stash". With Cydia 1.1.26, saurik has fixed the icon disappearing issue and has reorganised the end of the stashing feature. Following is the release note for Cydia 1.1.26
the latest version of Cydia Installer, launch Cydia, then tap on Reload button located at the top right corner. Wait for some time for the packages to load then search for the Cydia Installer package and update to new version. When you see a pop-up message saying "Essential Upgrade", just tap on "Complete Upgrade" to get the latest version of Cydia.
saurik is also working on updating the Eraser feature of Cydia Impactor. The tool erases all data on your device and reverts all changes to files on your iOS device, while removing the jailbreak. It also restores the stock iOS firmware. So in case something goes wrong with jailbreak, you can always use this tool to unjailbreak your device.
"Meanwhile, I've been spending most of my time for days working on updating the Eraser feature of Cydia Impactor to support iOS 9, as Pangu is now doing something more complex that I previously was not setup to "undo", in addition to Apple making some changes to the OTA format. I managed to get this done just in time, though I also ended up managing to do it without having to actually restore my device a eve once," confirms saurik.