Pass --accept-flake-config only during flake-related commands

[shivaraj-bh]

--accept-flake-config expects the flake to be already enabled, which will fail om health on systems with flake not enabled.

Error

❄️  nix --accept-flake-config --version️
Error: Unable to gather nix info

Caused by:
    0: Nix command error: Command error: Process exited unsuccessfully. exit_code=Some(1) stderr=error: experimental Nix feature 'flakes' is disabled; add '--extra-experimental-features flakes' to enable it

    1: Command error: Process exited unsuccessfully. exit_code=Some(1) stderr=error: experimental Nix feature 'flakes' is disabled; add '--extra-experimental-features flakes' to enable it

    2: Process exited unsuccessfully. exit_code=Some(1) stderr=error: experimental Nix feature 'flakes' is disabled; add '--extra-experimental-features flakes' to enable it

[srid]

I think we should just make the default accept_flake_config to be false, and instead set it to true in with_flakes().

[shivaraj-bh]

I think we should just make the default accept_flake_config to be false, and instead set it to true in with_flakes().

Done

[srid]

I just realized there's another bug in main ... --accept-flake-config is not even being passed in many places! Fixing this as part of this PR ...