Changing the CLI input file format to use `.toml` files

The MidenVM CLI uses a different file format to handle inputs to the VM. The CLI uses a JSON format with a `.inputs` file extension. The Miden compiler uses a slightly different `.toml` file extention format.

I wrote a basic tutorial of how to use the compiler here: https://github.com/0xPolygonMiden/miden-tutorials/pull/26/files?short_path=86b1b8d#diff-86b1b8d67d7b5c302b4154bb3158c58928fcc0688ff0e1b0705dc50ce950ccb1

In this tutorial I have to explain to the reader to create a new input file, which seems a bit clunky.

The miden compiler input file format looks like this:
```toml
[inputs]
stack = [2147482583]
```

Whereas the MidenVM file format looks like this:
```json
{
"operand_stack": ["2147482583"]
}
```

By making the MidenVM use the same input file format this would unify the input file formats of the VM and compiler.