Allowing duplicate links is failing when the flag is set to allow them

[langfob]

Here's the error output from a run where this failed and the project.yaml file had set the flag to allow duplicate links/spp ("duplicate_links_allowed: TRUE"):

...
About to create bpm matrix.

About to fill in bpm matrix.

indices (duplicates) = 35 38 57 58 83 85 89 93 94 103 107 113 114 120 124 126 127 129 132 134 135 141 142 143 144 146 149 150 157 160 163 165 166 168

duplicates =
from_node to_node
[1,] 10 18
[2,] 6 18
[3,] 26 42
[4,] 28 34
[5,] 20 28
[6,] 12 38
[7,] 12 36
[8,] 18 22
[9,] 12 44
[10,] 4 16
[11,] 6 40
[12,] 20 42
[13,] 12 26
[14,] 34 40
[15,] 14 18
[16,] 20 38
[17,] 2 14
[18,] 20 38
[19,] 4 18
[20,] 14 40
[21,] 6 20
[22,] 24 34
[23,] 32 34
[24,] 24 38
[25,] 2 18
[26,] 20 34
[27,] 6 26
[28,] 30 44
[29,] 14 40
[30,] 18 38
[31,] 2 18
[32,] 24 42
[33,] 14 36
[34,] 18 38

number of duplicates = 34

In stop_bdpg:

ERROR: 34 duplicate species in the Xu benchmark file.