Removed biradical singlets from R_MultipleBond Addition

After discussing with bbuesser and agvandeputte, we concluded a singlet
biradical would react much faster as a 1,2_cycloaddition than a regular
addition. There were no rules which used singlet biradicals (probably
because they do not react through this channel). I am only restricting
singlet biradicals for *3 atoms, I still allow them in R_R tree.

Groups were found by searching for the regex '\*3 .*2', which returned all
lines with *3 atoms that were birad (there were only 9 of them). Then I
manually searched them for biradical singlets.

Removed the following groups:
O_atom_singlet
CH2_singlet
NH_singlet

Changed *3 atom from 2 to 2T in the following groups:
Y_1centerbirad
CO_birad
Fixes to rule adj lists in Intra_R_Add_Endocyclic

There has been some confusion as to whether Cdd is a specific case of Cd.
In the current builds, they are exclusive. Thus many groups have had atoms
changed from Cd to {Cd, Cdd}. Here, I have copied over all the changes
which appeared in groups.py to the proper adj lists in rules.py. The
groups that changed were:

R5_SS_D (168 changes in rules)
R4_S_D (168 changes in rules)
R6_SMS_D (168 changes in rules)
R5_SD_D (1 change in rules)
R6_SSS_D (168 changes in rules)
R3_D (1 change in rules)

A few of the more general groups had the above change and nitrogen added
to their definition:

R3_D (1 change in rules)
top node, multiplebond_intra changed to include N and Cdd