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Run Sage once as root:

sudo ./sage --nodotsage

This will give Sage the permissions it needs to update the paths. Afterwards, you will be able to run Sage as a normal user.

As of commit 8f99d8, you can use any JQuery selector, including ones that select multiple elements, as an inputLocation. You can create a Sage cell in multiple locations using something like:

sagecell.makeSagecell({inputLocation:  '.sagecell-plot',
                       template:       sagecell.templates.restricted});

where sagecell-plot is the name of the class of which each of the inputLocations is a member.