In order to handle all files (mainly in dataroot) properly, some changes have landed to 2.6 and upwards (
From that issue it was clear that some new "rules" should be observed when handling files and some functions should be used as best candidates. So MDLSITE-2345 was created, just to verify developers observe those (complex) rules.
Then Damyon came with a very good idea, about to create some core_io (or core_iofs IMO) wrapper to allow developers to have a simpler API for all fs operations. Such wrapper will be in charge of observing all those umask/chmod rules, hopefully in a transparent way. And, at the same time, it would be really easy to detect any violation (not using the wrapper).
So this issue is about to discuss and implement that io[fs] wrapper. And apply it everywhere.