Find a more consistent terminology

[Bernhard10]

Sometimes we use node, sometiem element for coarse grained elements.

E.g. get_node_from_residue_num and nucleotides_to_elements do similar things but have different names.

Also the words loop, bulge, stem, element, interior loop are sometimes used incorrectly/ inconsistently

Do we call "i1", "s0", ... element names?

[Bernhard10]

Another example is fasta/ fastax/ ss_fasta.

Do we make a difference between fasta files and fasta+structure files?

[Bernhard10]

For forgi 2.0, I tried to use elem for the keys to rna.defines and define only for the values (i.e. list of ints)

[Bernhard10]

For forgi 3.0, we should again check the terminology and make it even more consistent.