Found one Java-level deadlock:
=============================
"Thread-12678585":
  waiting to lock monitor 0x4212841c (object 0x5b87b6c8, a dan200.computer.core.Computer),
  which is held by "Server thread"
"Server thread":
  waiting to lock monitor 0x42dc14bc (object 0x5b8874b8, a [Ldan200.computer.core.apis.PeripheralAPI$PeripheralWrapper;),
  which is held by "Thread-12678585"

Java stack information for the threads listed above:
===================================================
"Thread-12678585":
        at dan200.computer.core.Computer.getID(Computer.java:379)
        - waiting to lock <0x5b87b6c8> (a dan200.computer.core.Computer)
        at dan200.computer.core.Computer$APIEnvironment.getComputerID(Computer.java:70)
        at dan200.computer.core.apis.PeripheralAPI$PeripheralWrapper.getID(PeripheralAPI.java:214)
        - locked <0xafeeb670> (a dan200.computer.core.apis.PeripheralAPI$PeripheralWrapper)
        at openperipheral.core.peripheral.HostedPeripheral.attach(HostedPeripheral.java:209)
        at dan200.computer.core.apis.PeripheralAPI$PeripheralWrapper.attach(PeripheralAPI.java:82)
        - locked <0xafeeb670> (a dan200.computer.core.apis.PeripheralAPI$PeripheralWrapper)
        at dan200.computer.core.apis.PeripheralAPI$2.execute(PeripheralAPI.java:308)
        - locked <0x5b8874b8> (a [Ldan200.computer.core.apis.PeripheralAPI$PeripheralWrapper;)
        at dan200.computer.core.ComputerThread$1$1.run(ComputerThread.java:117)
        at java.lang.Thread.run(Thread.java:724)
"Server thread":
        at dan200.computer.core.apis.PeripheralAPI.advance(PeripheralAPI.java:351)
        - waiting to lock <0x5b8874b8> (a [Ldan200.computer.core.apis.PeripheralAPI$PeripheralWrapper;)
        at dan200.computer.core.Computer.advance(Computer.java:511)
        - locked <0x5b8a4470> (a java.util.ArrayList)
        - locked <0x5b87b6c8> (a dan200.computer.core.Computer)
        at dan200.computer.shared.NetworkedComputerHelper.update(NetworkedComputerHelper.java:128)
        at dan200.turtle.shared.TileEntityTurtle.func_70316_g(TileEntityTurtle.java:2458)
        at net.minecraft.world.World.func_72939_s(World.java:2204)
        at net.minecraft.world.WorldServer.func_72939_s(WorldServer.java:548)
        at net.minecraft.server.MinecraftServer.func_71190_q(MinecraftServer.java:666)
        at net.minecraft.server.dedicated.DedicatedServer.func_71190_q(DedicatedServer.java:275)
        at net.minecraft.server.MinecraftServer.func_71217_p(MinecraftServer.java:585)
        at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:482)
        at net.minecraft.server.ThreadMinecraftServer.run(SourceFile:582)

Found 1 deadlock.