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[Code scan] Make dpdisp-submit skill commands honor --allow-ref #619

Description

@njzjz

Found by a Codex global repository scan of deepmodeling/dpdispatcher at commit 98a9e08.

Problem
The dpdisp-submit skill says $ref configs require --allow-ref, but the mandatory validation and submission command chain omits that flag.

Relevant code

### Validate & Submit
You **MUST** strictly execute the following command chain in sequence.
**Note**: If the `$ref` syntax is used in the configuration, you must pass the `--allow-ref` flag to all validation and submission commands, otherwise parsing or validation will fail even if the JSON content is correct.
```bash
# Logic and Schema Validation
uvx --with dpdispatcher dargs check -f dpdispatcher.entrypoints.submit.submission_args submission.json
# Submit Job
uvx --from dpdispatcher dpdisp submit submission.json
```

Impact
Agents or users following the skill exactly will reject valid $ref-based submission configs during validation or submission, despite the note immediately above the commands.

Suggested fix
Include --allow-ref in the command chain when $ref is used, or show separate command chains for referenced and non-referenced configs.

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