What is this error, and can/should it be eliminated?

[Server] INFO Please note that the working directory for scriptcraft v3.2.0-2016-03-19 is /scriptcraft
[Server] WARN Please put plugins in the /scriptcraft/plugins directory
[Server] WARN Legacy ScriptCraft directory /plugins/scriptcraft was found. This directory is no longer used.
[Server] WARN cow-clicker minigame is not yet supported in CanaryMod or Craftbukkit
[Server] WARN Could not connect to dev.bukkit.org, please try again later.
[Server] WARN :1:1: Premature end of file.
[Server] INFO No updates found!
[Server] WARN The updater could not find any files for the project id 31279
[Server] INFO Enabling scriptcraft v3.2.0-2016-03-19

I've never seen this message: The updater could not find any files for the project id 31279

All of these pages indicate this is an issue with Update routines that seem to be looking for an update from their home site, a Bukkit site, etc.. Given the other error about dev.bukkit.org and the confirmation for "No updates found!", I'm guessing it's related to that.
HTH

http://www.minecraftserverhost.net/forum/viewtopic.php?t=1710&p=3479
PEXPlugins/PermissionsEx#2495
games647/LagMonitor#12

This message is generated by an updater running in the PermissionsEx plugin (see PEXPlugins/PermissionsEx#2495 , and for the specific line of code: https://github.com/gravitylow/Updater/blob/a857fd9/src/main/java/net/gravitydevelopment/updater/Updater.java#L677). It has nothing to do with ScriptCraft, so I believe this issue and #308 can be closed.

Agreed. Thanks!!