Add --dir option to run.md

[Airthee]

We can see that some options are only available in CLI --help command but not in the documentation.
I noticed that the --dir is usefull so I wanted to add it.

Maybe there are other options that should be added ?

[stackblitz[bot]]

Run & review this pull request in StackBlitz Codeflow.

[vercel[bot]]

@Airthee is attempting to deploy a commit to the pnpm Team on Vercel.

A member of the Team first needs to authorize it.

[zkochan]

That option is available on all commands and is documented on this page: https://pnpm.io/pnpm-cli

[Airthee]

Thanks I didn't see it...