Fix various pVACvector issues

[susannasiebert]

• The junction_scores.best_spacers.tsv and junction_scores.tsv intermediate files are currently identical. We should write a file that summarizes all the passing junctions at that point in the run, including spacers.
• The -k flag is not respected for each iteration and the tmp file for each are currently deleted
• Ensure that a log file of the inputs for the whole run gets created and checked against
• Update some wording for "increasing the acceptable junction binding score to allow more possible connections (-b parameter)". The parameter should be decreased. Also add more detail to explain how the -b parameter impacts this.
• Update the wording "No valid path found. No valid junction between peptides:" to add more context.
• Add some sort of success messages, if we find a path
• Temperature Energy Accept Improve Elapsed Remaining is written to to stderr instead of stdout
• Use the percentile cutoff, if provided.