The suicide clause was something i introduced to Ponychan, long before Ponyville came about, to protect the community from liability that arose from numerous suicide threads.
The issue then, and now, is thus: the administration and the moderatorship are not trained in suicide prevention or similar such techniques. Suicide threads, even if uncommon, absolutely do come up.
On Ponychan, what happened was, the staff had reason to suspect that a poster of a suicide thread had actually committed suicide, and had posted a thread seeking comfort or help of some kind, though perhaps not in such a direct manner.
The site's community at the time, though well intentioned, came up with all kinds of advice and psychoanalysis and such.
When the person therein had potentially killed themselves, that well intentioned advice, or trolling, or whathave you, became a danger to the site, and showed just how dangerous an instantaneous imageboard environment could be to a psychologically unstable person.
Take, for example, a suicide thread in which an OP says they cannot take life anymore and wants to kill themselves.
Let us say then, an anonymous troll, says "do it." And before a moderator can get to it, the OP sees it and follows through. This sort of situation doesn't just open us up to substantial liability, it is dangerous too for the individual who, in a moment of weakness, sought help from a dangerous place: a place that allows the unaccountable nature of anonymity.
The clause is not meant to discourage users from seeking comfort, but it is meant to protect the site front liability, and the user from perhaps seeking care from an environment of substantial risk.
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