Workflow outputs (third preview)

[bentsherman]

This PR implements the third preview of the workflow output definition for Nextflow 25.04.

Changes are described in the docs, copied here for convenience:

• The publish: section can only be specified in the entry workflow.

• Workflow outputs in the publish: section are assigned instead of using the >> operator. The output name must be a valid identifier.

• By default, output files are published to the base output directory, rather than a subdirectory corresponding to the output name.

• The syntax for dynamic publish paths has changed. Instead of defining a closure that returns a closure with the path directive, the outer closure should use the >> operator to publish individual files.

• The mapper index directive has been removed. Use a map operator in the workflow body instead.

Changes not described in the docs:

• The onWorkflowPublish trace event has been modified to include the output name. It is emitted once for each output, rather than once for each channel value, and it is emitted regardless of whether the index file is enabled.

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[bentsherman]

@pditommaso regarding this change to onWorkflowPublish

Aside from the fact that it's a preview feature, there is a bigger issue I wanted to raise about the TraceObserver -- these overloads that we add to be backwards compatible don't actually work

Even if we add something like this:

void onWorkflowPublish(Object value) {
    onWorkflowPublish(null, value)
}

If I build a plugin with Nextflow 24.10 and try to use it with 25.04, it will fail with an error like this:

ERROR ~ Receiver class nextflow.validation.ValidationObserver does not define or inherit an implementation of the resolved method 'abstract void onWorkflowPublish(java.lang.String,java.lang.Object)' of interface nextflow.trace.TraceObserver.

This is because the custom trace observer gets compiled against the 24.10 version of TraceObserver and run against the 25.04 version at runtime, but it doesn't receive the new method overload. I think it's a limitation of the Java/Groovy runtime.

So there is no point in adding these extra overloads. Plugins built with an older Nextflow will break no matter what we do

See: nextflow-io/nf-schema#90