I had (well, still have) Skype Portable 6.10.0.104. It was nagging me to upgrade, but I always let PortableApps upgrade the apps, so I ignored Skype's request at first. But PortableApps's Apps->Check For Updates did not report Skype as being one of the apps that needed updating.
After a while I couldn't stand it anymore, so I let Skype do what it wanted to do. Unfortunately it installed a fresh copy of Skype (not Portable) 6.11.0.102, which of course is not what I wanted. So now I have both.
Why isn't the PA platform seeing the same need for an upgrade that the Skype program inside it was seeing? And what should I do now? Fortunately most of the data associated with Skype is online rather than local, so it doesn't matter too much if I'm a bit schizophrenic in my use of the two until this is figured out.
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Outdated Official Portable Applications
Somehow I didn't realize that every version of each application needed to be customized to make it work with PA - I guess I thought there was some wrapper that was somewhat separate. But thinking about it, it makes total sense - every place where the code reads/writes the registry must be changed, for example. In the future I'll be more patient (and more determined in clicking "Not now" when apps try to get me to upgrade apart from PA), and I guess it's safe to uninstall the non-PA copy of Skype, since it wouldn't know about the location of any of the Skype Portable files. Thanks for the link.
It's usually a mater of dropping it in. Some apps require scripting updating that takes a few hours (Firefox, Thunderbird, LibreOffice, etc). Other apps require tons of manual work when they change all kinds of functionality and file placement (see: Skype).
Sometimes, the impossible can become possible, if you're awesome!
Well, whether it's a little or a lot of work, on behalf of all the users, thanks and applause go out to the developers who do this!