The bisect_distance in the mirror modifier was hardcoded to 0.001.
This would result in some unexpected behaviour like vertices close
to the mirror plane being deleted or merged.
The fix changes the distance to 1e-7 to avoid any unintentional
"merging".
EDIT: The fix now adds a parameter to the mirror modifier to expose the
bisect distance to the user. The default is set to the previous hardcoded
value to not "change" previous files.