Cydia 1.1.26 is a bug fix release
Modification to Core Stash Logic
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 :/.