Update help

Author: tamuri

src/resources/help.txt

@@ -3,12 +3,10 @@ OPTIONS
        -n, -name
               Specifies name for the run. Output files are prefixed with this name.
               Be careful! The program will overwrite files with the same name.
-              // todo: Exit if files with same name exit
 
        -s, -sequences
               Coding sequences alignment file name in PHYLIP format. Spaces are
               not allowed in sequence names.
-              // todo: Other MSA formats esp. FASTA
 
        -t, -tree
               Newick-formatted tree file name. The tree string can be supplied
@@ -53,8 +51,6 @@ OPTIONS
               It is recommended that you do not construct these by hand but
               rather use the output generated by the program itself.
               DEFAULT: [0]
-              // todo: Need to make sure the right amino acid has fitness fixed
-              // todo: to 0 when user provides fitness vector
 
    Optimisation
        -fix