[BUG] Argdump `store_true`/`store_false` mutually exclusive flags with same `dest` creates weird Boutiques descriptor

[michellewang]

I get this Boutiques descriptor from the argdump below. It has a few problems:

1. Inputs are not mutually exclusive
2. The second input is called hires_or_hires and has two identical entries in value-choices

I expect a single input submm_recon_or_no_submm_recon instead, with nested inputs that are both flags.

{
  "schema-version": "0.5+styx",
  "name": "petprep",
  "description": "PETPrep: PET PREProcessing workflows v0.1.dev1+g2f5176c",
  "command-line": "petprep [SUBMM_RECON] [HIRES_OR_HIRES]",
  "inputs": [
    {
      "id": "submm_recon",
      "type": "Flag",
      "value-key": "[SUBMM_RECON]",
      "description": "Enable FreeSurfer sub-millimeter (hires) reconstruction.",
      "optional": true,
      "command-line-flag": "--submm-recon",
      "name": "submm_recon"
    },
    {
      "id": "hires_or_hires",
      "type": "String",
      "value-key": "[HIRES_OR_HIRES]",
      "optional": true,
      "value-choices": [
        "--no-submm-recon",
        "--no-submm-recon"
      ],
      "name": "hires_or_hires"
    }
  ]
}

This is likely due to the argdump having:

    "mutually_exclusive_groups": [
      {
        "actions": [
          "hires",
          "hires"
        ]
      }
    ]

Argdump input:

  {
    "$schema": "https://niwrap.dev/argdump/schema-v1.json",
    "$env": {
      "python_version": "3.13.15",
      "python_implementation": "CPython",
      "platform_system": "Linux",
      "platform_release": "6.17.0-1022-azure",
      "platform_machine": "x86_64",
      "argdump_version": "0.1.3"
    },
    "prog": "petprep",
    "description": "PETPrep: PET PREProcessing workflows v0.1.dev1+g2f5176c",
    "formatter_class": "ArgumentDefaultsHelpFormatter",
    "actions": [
      {
        "option_strings": [
          "--submm-recon"
        ],
        "dest": "hires",
        "action_type": "store_true",
        "nargs": 0,
        "const": true,
        "default": false,
        "help": "Enable FreeSurfer sub-millimeter (hires) reconstruction."
      },
      {
        "option_strings": [
          "--no-submm-recon"
        ],
        "dest": "hires",
        "action_type": "store_false",
        "nargs": 0,
        "const": false,
        "default": true,
        "help": "Disable FreeSurfer sub-millimeter (hires) reconstruction."
      }
   ],
    "mutually_exclusive_groups": [
      {
        "actions": [
          "hires",
          "hires"
        ]
      }
    ]
  }

[nx10]

Fixed in #90, structurally. Your dump now produces a single submm_recon_or_no_submm_recon input with both flags as distinct choices, exclusive, and no stray Flag alongside it.

["hires","hires"] means two members share that dest, whereas a dest listed once means only one of its actions is a member. We now use that, which also stops an unrelated same-dest action being dragged into a group.

Still open: the arms are value-choices rather than nested flags. Will comment on more on this in #89