gnuplot plotting multiple line graphs

I think your problem is your version numbers. Try making 8.1 --> 8.01, and so forth. That should put the points in the right order.

Alternatively, you could plot using X, where X is the column number you want, instead of using 1:X. That will plot those values on the y axis and integers on the x axis. Try:

plot "ls.dat" using 2 title 'Removed' with lines, \
     "ls.dat" using 3 title 'Added' with lines, \
     "ls.dat" using 4 title 'Modified' with lines

andyras is completely correct. One minor addition, try this (for example)

plot 'ls.dat' using 4:xtic(1)

This will keep your datafile in the correct order, but also preserve your version tic labels on the x-axis.