Follow-up to #11195

When running JabRef using gradle, one gets following outputs:

WARNING: Unknown module: org.jabref.merged.module specified to --add-exports
WARNING: Unknown module: org.jabref.merged.module specified to --add-exports
WARNING: Unknown module: org.jabref.merged.module specified to --add-opens
WARNING: Unknown module: org.jabref.merged.module specified to --add-opens
WARNING: Unknown module: org.jabref.merged.module specified to --add-opens

They are caused by our new applicationDefaultJvmArgs entry. That entry is needed for our jpackage task.

However, for run, they are not needed. Thus, this PR adds a "hot patch" to the run task to avoid that output.

Mandatory checks

• Change in CHANGELOG.md described in a way that is understandable for the average user (if applicable)
• Tests created for changes (if applicable)
• Manually tested changed features in running JabRef (always required)
• Screenshots added in PR description (for UI changes)
• Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
• Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.