fix: lock down allow-run permissions more

[dsherret]

--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
2. 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.

This also fixes #25171 but I'll open a separate PR to add tests for that and close that issue.

[bartlomieju]

Looks okay, other than than one problem