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Close #6540

This PR moves the Nextflow version check (manifest.nextflowVersion) so that it happens as early as possible -- immediately after the config is loaded

This will improve the error message for errors that are downstream of a version mismatch. For example, in the linked issue, a pipeline requiring >=25.10 was run with 25.04, and because it was also loading a plugin that requires >=25.10, the resulting error was about the plugin not existing rather than the Nextflow version being incorrect

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return result
}

/**
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Shouldn't be better to create an independent class in nf-commons, in case it is required for other commands or plugins in the future?

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Good idea, likely it will be used by both CLI v1 and CLI v2

CmdRun also has logic for (1) resolving the script file and (2) resolving CLI params. These could also be moved into helper classes in the future for the same reason. I will keep this in mind for CLI v2

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@jorgee on second thought, it might be better to keep the logic in CmdRun for now. I'm not sure at this point what the right interface should be for a separate class -- should it take the config map? or a Manifest? or a version string? The answer will become clear when new features like CLI v2 need to re-use this logic.

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Nextflow version check happens after loading the plugins

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