fix(flags): correct deprecation notices

[iuioiua]

Fixes #4203

Normally, we'd call parseArgs() within parse(). However, parseArgs() is so complex with all its type arguments, one cannot simply do so. I figured the next best thing to do is copy the entire std/cli/parse_args.ts implementation. I did this instead of reverting to the old std/flags code, as the new code has minor tweaks that enable the noUncheckedIndexedAccess compiler option.

[kt3k]

LGTM