This PR refactors "cli/flags.rs" and "runtime/permissions.rs" so
that "allow_read", "allow_write" and "allow_net" themselves
have allowlists, instead of storing them in additional fields.
This commit moves following tools into a single "tools"
module located at "cli/tools/mod.rs":
- formatter
- linter
- test runner
- coverage collector
- installer
- binary upgrader
- repl