I think there was a checkbox during installation which you had to select if you wanted to have the folders of your projects outside your home directory. If you didn't select it during installation, you have to put your projects folders inside your home directory ;)
I Think they just haven't forced that restriction in the emulator, but I expect you won't be able to "run" more than 9 apps on the phone. Remember it's an alpha sdk :) I guess the restriction wasn't implemented yet when they released the alpha sdk :)
I don't know about the stack issue, but about the apps:Sailfish OS allows a max of 9 apps on the homescreen. That's a design choice they made
Go to about->plugins in Sailfish qtcreator, and enable Mer target ;) restart Qtcreator. Then go to settings->kits and clone the (uneditable) sailfish kit you'll find
Which is the most likely solution it seems, at least from the info we got at jolla love day
Where did you the jolla has HD re
Maybe you forgot to add it to the qml.files variable in the .pro file? Or to the .qrc, if you're using resources :)