refactor(cli): Integrate standalone mode cert handling into `Flags` (#17419)

The way the standalone mode handles the `--cert` flag is different to
all other modes. This is because `--cert` takes a path to the
certificate file, which is directly added to the root cert store; except
for compile mode, where its byte contents are stored in the standalone
metadata, and they are added to the root cert store after the
`ProcState` is created.

This change instead changes `Flags::ca_file` (an `Option<String>`) into
`Flags::ca_data`, which can represent a `String` file path or a
`Vec<u8>` with the certificate contents. That way, standalone mode can
create a `ProcState` whose root cert store alreay contains the
certificate.

This change also adds a tests for certificates in standalone mode, since
there weren't any before.

This refactor will help with implementing web workers in standalone mode
in the future.

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