Standardize directory names

Reorganized.  Created a new top level include directory that will hold all of Trick's header files. Moved all of the Trick headers to this directory.  Created a libexec directory that holds all of the executables that users don't need to execute directly.  Changed all of the executables remaining in bin to start with "trick-".  In the sim_services directories changed all source files to find the Trick headers in their new location.  Since all of the include files are gone in sim_services, removed the src directories as well, moving all of the source files up a level.  Moved the makefiles, docs, man, and other architecture independent files into a top level share directory.  Renamed lib_${TRICK_HOST_CPU} to lib64 or lib depending on the platform we're currently on.

refs #63

trick_source/sim_services/VariableServer/VariableServerThread_restart.cpp

@@ -0,0 +1,41 @@
+
+#include <stdlib.h>
+#include "trick/VariableServerThread.hh"
+
+void Trick::VariableServerThread::preload_checkpoint() {
+    // Let the thread complete any data copying it has to do
+    // and then suspend data copying until the checkpoint is reloaded.
+    pthread_mutex_lock(&copy_mutex);
+
+    // Save the pause state of this thread.
+    saved_pause_cmd = pause_cmd;
+
+    // Disallow data writing.
+    pause_cmd = true ;
+
+    // Temporarily "disconnect" the variable references from Trick Managed Memory
+    // by tagging each as a "bad reference".
+    std::vector <VariableReference *>::iterator it ;
+    for (it = vars.begin(); it != vars.end() ; it++) {
+        (*it)->ref->address = (char*)&bad_ref_int;
+        (*it)->ref->attr = new ATTRIBUTES() ;
+        (*it)->ref->attr->type = TRICK_NUMBER_OF_TYPES ;
+        (*it)->ref->attr->units = (char *)"--" ;
+        (*it)->ref->attr->size = sizeof(int) ;
+    }
+}
+
+void Trick::VariableServerThread::restart() {
+    // Set the pause state of this thread back to its "pre-checkpoint reload" state.
+    pause_cmd = saved_pause_cmd ;
+
+    // Set retry_bad_ref so that variables in this varible server thread will
+    // be re-resolved to the newly re-created memory objects.
+    var_retry_bad_ref();
+
+    // Allow data copying to continue.
+    pthread_mutex_unlock(&copy_mutex);
+
+}
+
+