About five minutes after submitting issue #2 I worked out a solution! This should fix both #2 and #1.

This changes the recommended plugin usage from:

config.env.enable

To:

config.env.enable __FILE__

I'd prefer not to have to do that, but I can't work out how to get the path to the Vagrantfile. (Maybe someone with better knowledge of Vagrant internals can fix that...) In the mean time, the original method (with no parameters) will still work and still have the same effect it used to - looking in the current working directory instead of the Vagrantfile directory.

I also added three low-level methods to allow the user to call Dotenv methods directly:

config.env.load '/path/to/.anotherenv'
config.env.load! '/path/to/.env'
config.env.overload '/path/to/.env'

See the dotenv source comments for explanations of these three methods. (They don't seem to be documented anywhere else...) Note that these paths are relative to the current working directory, so File.dirname(__FILE__) may be called for here.