`--allow-run` even with an allow list has essentially been
`--allow-all`... this locks it down more.
1. Resolves allow list for `--allow-run=` on startup to an absolute
path, then uses these paths when evaluating if a command can execute.
Also, adds these paths to `--deny-write`
1. Resolves the environment (cwd and env vars) before evaluating
permissions and before executing a command. Then uses this environment
to evaluate the permissions and then evaluate the command.
