Fix deprecations (#59)

In the massive deletion of deprecated functions when rc1 was released (#59),
`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).
OK - I suspected so. But as I said, I didn't dig deeper into what various parts of the code did, so I figured it was better to just replace everywhere.