Bridge zombienet tests: remove old command (#5434)

Related to: https://github.com/paritytech/polkadot-sdk/issues/3176

This PR:
- migrates test 0003 to the new bridges zombienet tests command
**This test didn't work before and it still doesn't work. It was added
at a time when we couldn't run it because we didn't have the scafolding.
It needs to be fixed. For the moment we keep it in the repo as it is
since the idea has value. But we don't run it in the CI. We can also
decide to remove it in the future**
- removes the old command for running bridge zombienet tests
- updates the README