cosmetic changes in attempt to make the code structure clearer

[LeilyR]

cosmetic changes in attempt to make the code structure clearer

[lldelisle]

Hi, I am just wondering if for retrocompatibility issues, bin/make_tracks_file should not print a message that it is now called make_tracks_config. Also I think in the parser we can change --tracks to --tracksConfig. --tracks will still work but in our examples we use --tracksConfig which is more clear.