[docs-v2] suggestions for 'running' sections

[jfy133]

Got to mid-way through 'nextflow for your system'.

Also need to add TODOs on these thoughts:

• Running > Reference Genomes: I've moved the 'local genome' section first, as I think that is the most inclsuive and common method (iGenomnes only works specifically for essnetial model organisms)
• Running > Reference GEnomes > RefGenie: The RefGenie instructions I'm suspicious of, it refers to the tool maknig a Nextflow config but I see no reference to this on the refgeni website (but note that the instructions are the same on the current docs site), [we need to find who wrote those... bgit glame isn't helping]
• Running > Running pipelines offline: I don't understand what it means by 'copy the plugins' from where do oyu see the list of plugins? [again need the author to clarify]
• Running > Running pipelines offline > Transfer reference genomes offline: link to Reference genomes is dead
• running/configuration/overview > I feel the 'Nextflow loads configuration parameters sequentially and overwrites previous values. The loading order is:' should go first, because this applies to everything (e.g. you can give a -c even if you've also given a -profile)
• running/configuration/overview: Is Parameters in custom.config files will not override defaults in nextflow.config. Use -params-file with YAML or JSON format instead. correct? I'm pretty sure nextflow.coinfig is even more base that base.conf

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