Varied fixes to get linux running. Allow for shutdown on linux.

dev/ide_disk.cc:
    Fix to PIO writes and also add command needed for shutdown
dev/pcidev.cc:
    Change the panic on write to read-only registers to a debug print.  The
    kernel tries to write back over all of the PCI registers to restore
    the saved SRM state, so we need to let it do this without panicing.
sim/system.cc:
    Add back increment of number of running systems to allow trap of halt
    work correctly.

--HG--
extra : convert_revision : 84aba4effbec14545f3610c19a8e321d7e7f7cf2

sim/system.cc

@@ -52,6 +52,9 @@ System::System(const std::string _name,
       bin(_bin),
       binned_fns(binned_fns)
 {
+    // increment the number of running systems
+    numSystemsRunning++;
+
     // add self to global system list
     systemList.push_back(this);
     if (bin == true) {