first of all: YES use SSH.
to upgrade manually:
ssh into api
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sudo apt-get -y update &
sudo apt-get -y upgrade &
that does upgrades to existing installed programs ( cd pibeacon; sudo python installLibs.py force & does that for you on the RPI)
But I suggest to use the manual way. you might see an error message
if you want to get the latest RPI OPSYS image with ALL programs apps etc you need to do:
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sudo apt-get -y update &
sudo apt-get dist-upgrade &
(no -y in 2. line). but many of them are not needed AND THIS WILL TAKE SOME HOURS !!
I do not suggest to download a fresh copy from raspberry as there are many libs needed by pibeacon you would need to be install manually.
The latest posted SSD (November2016 ) in downloads has all the new RPi version and configs libs .. installed. (it took me a day to create that one with all downloads, sizing, imaging redoing things ....)
I have ~15 RPI. Some of them are still on the original SSD (feb this year) and some have the latest. All of them work.
Whenever I have an issue on an RPI, I pop in the latest SSD . But then I need to set the network config on a monitor when I use WiFi on the RPI.
anyway if it works don't break it .. but the new pibeacon has some really nice features with groups and significant reduced CPU on the indigo server when you use i7
so if you like to tinker . download the new SSD from the pibeacon download, configure network, . that should be it.
you could also just use the new pibeacon plugin
hope that answers your questions..
Karl