Fix deprecations (#59)

In the massive deletion of deprecated functions when rc1 was released,
`Base.has`, `Base.ref` and `Base.assign` were removed.

I've simply find/replaced them with their replacements (`haskey`, `getindex`
and `setindex!`), so I might very well have introduced new problems here,
but all tests pass and my own debugging was able to progress smoothly (where
it previously broke as soon as I tried to print something).