As we wish, Cydia founder Saurik just brought a major update to Cydia Installer with couple of updates. New Cydia Installer 1.1.25 now moves the jailbreak content to the user partition from the system partition. This is why you will see “Preparing Filesystem” message when you launched Cydia Store for the first time after jailbreaking, because Cydia did not complete the jailbreak content transfer from the system partition to the user partition.
Below is the Cydia 1.1.26 release notes by Saurik
I wrote this stash logic in 2008, and have made minimal modifications to it since (with only one even remotely major change, last year, to deal with data protection flags). This code has been used to stash /Applications on every jailbreak since then (including jailbreaks where the stash step was executed on the data extracted in an IPSW file on a computer, such as PwnageTool). I could easily imagine it has been used one billion times, which is why I generally like to trust this code. However, people are now relying on it to do a “late stash” of a key folder (Applications), and thereby are more likely to be doing other things while this happens without realizing that this is about to be really important, and I’m seeing a couple reports of some application icons disappearing. This is all the more likely due to Cydia iself being something the user was just using to upgrade Cydia, and then the user relauches it right after the upgrade. I have thereby reorganized the end of the stashing feature to have a much much much much shorter window of opportunity during which anything can go wrong and am hastily pushing an update :/.
Download Cydia 1.1.26, course you do not have to manually download it to get the update, you only need to re-run the Cydia app on your jailbroken device to get the update automatically. Once the Cydia 1.1.26 updated, it will perform a “Preparing Filesystem” to move the jailbreak content to the user partition from the system partition.
Please note that avoid installing the update for Cydia Installer with the update for Pangu 9.0.x Untether package as we’ve heard that it causes issues.
In addition, Saurik has also confirmed that he is working on Cydia Impactor for iOS 9, which allows you to remove the data and all your personal data without having to restore your device.