Revisit Repo initialization

[wdbaruni]

The repo is initialized in the RootCmd before any flags are registered. This means only default configurations are used when initializing the repo and any env variables or flags will be ignored. For example, if I run bacalhau serve --compute-execution-store-path my-awesome-path for the very first time, then bacalhau will still initialize the repo with default value, create ~/.bacalhau/compute-store directory, and create config.yaml with ~/.bacalhau/compute-store instead of my provided one. It is difficult to do things differently with our current setup as we initialize the repo in any command, but these flags are only available for serve command

Reference: #3429

[wdbaruni]

Will be addressed as part of #4014