Embedders may have special requirements around file opening, so we add a
new `check_open` permission check that is called as part of the file
open process.
1. Stops `deno publish` using some custom include/exclude behaviour from
other sub commands
2. Takes ancestor directories into account when resolving gitignore
3. Backards compatible change that adds ability to unexclude an exclude
by using a negated glob at a more specific level for all sub commands
(see https://github.com/denoland/deno_config/pull/44).
