Plugin upgrade utility should not upgrade plugins not mentioned in the tsv file when used from the command line

[johann-petrak]

Currently, the utility will upgrade plugins not mentioned in the TSV file according to the GATE version it runs under.

When running from the command line for a large number of pipelines, using a tsv file this is hard to control and would require to first find all plugins and plugin versions that exist anywhere in any pipeline file and add all of them with the appropriate SKIP in the tsv file.

It would be better if the utility simply only performs the upgrades mentioned in the tsv file if a tsv file is given and do the automatic upgrades only if no tsv file is given.