make doxygen broken

Updated the directory names in the doxygen files to match the new directory locations
of our source code files.  The documentation builds now.  But we still need to
remove the duplicate documentation that is now in the wiki, because the wiki is
more up to date.

refs #158

doxygen/.gitignore

@@ -1 +1,2 @@
 warning_msgs
+html

doxygen/Doxyfile

@@ -1687,7 +1687,7 @@ TAGFILES               =
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create
 # a tag file that is based on the input files it reads.
 
-GENERATE_TAGFILE       = $(TRICK_HOME)/docs/trick.tag
+GENERATE_TAGFILE       = $(TRICK_HOME)/share/doc/trick/trick.tag
 
 # If the ALLEXTERNALS tag is set to YES all external classes will be listed
 # in the class index. If set to NO only the inherited external classes

doxygen/Doxyfile_rtf_users_guide

@@ -1687,7 +1687,7 @@ TAGFILES               =
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create
 # a tag file that is based on the input files it reads.
 
-GENERATE_TAGFILE       = $(TRICK_HOME)/docs/trick.tag
+GENERATE_TAGFILE       = $(TRICK_HOME)/share/doc/trick/trick.tag
 
 # If the ALLEXTERNALS tag is set to YES all external classes will be listed
 # in the class index. If set to NO only the inherited external classes

doxygen/design/main_page.dox_in

@@ -30,14 +30,14 @@
 
 // section 3
 #include "run_sim.dox_in"
-#include "sim_services/Executive/design.dox_in"
+#include "sim_services/Executive/docs/design.dox_in"
 #include "sim_services/ScheduledJobQueue/design.dox_in"
-#include "sim_services/RealtimeSync/design.dox_in"
-#include "sim_services/Clock/design.dox_in"
-#include "sim_services/Timer/design.dox_in"
-#include "sim_services/DataRecord/design.dox_in"
-#include "sim_services/CommandLineArguments/design.dox_in"
-#include "sim_services/MonteCarlo/design.dox_in"
+#include "sim_services/RealtimeSync/docs/design.dox_in"
+#include "sim_services/Clock/docs/design.dox_in"
+#include "sim_services/Timer/docs/design.dox_in"
+#include "sim_services/DataRecord/docs/design.dox_in"
+#include "sim_services/CommandLineArguments/docs/design.dox_in"
+#include "sim_services/MonteCarlo/docs/design.dox_in"
 #include "sim_services/Integrator/design.dox_in"
 
 // section 4

doxygen/makefile

@@ -1,6 +1,6 @@
 
-export TRICK_DOCS = $(TRICK_HOME)/docs
-export TRICK_RELEASE = $(shell $(TRICK_HOME)/bin/trick_version -v)
+export TRICK_DOCS = $(TRICK_HOME)/share/doc/trick
+export TRICK_RELEASE = $(shell $(TRICK_HOME)/bin/trick-version -v)
 export TRICK_MAJOR = $(shell echo $(TRICK_RELEASE) | cut -f 1 -d.)
 export TRICK_MINOR = $(shell echo $(TRICK_RELEASE) | cut -f 2 -d.)
 

doxygen/requirements/main_page.dox_in

@@ -48,12 +48,12 @@
 // section 3
 #include "software_description.dox_in"
 #include "functional_requirements.dox_in"
-#include "sim_services/Executive/requirements.dox_in"
+#include "sim_services/Executive/docs/requirements.dox_in"
 #include "sim_services/ScheduledJobQueue/requirements.dox_in"
-#include "sim_services/RealtimeSync/requirements.dox_in"
-#include "sim_services/Clock/requirements.dox_in"
-#include "sim_services/Timer/requirements.dox_in"
-#include "sim_services/CommandLineArguments/requirements.dox_in"
+#include "sim_services/RealtimeSync/docs/requirements.dox_in"
+#include "sim_services/Clock/docs/requirements.dox_in"
+#include "sim_services/Timer/docs/requirements.dox_in"
+#include "sim_services/CommandLineArguments/docs/requirements.dox_in"
 #include "required_states.dox_in"
 #include "software_interfaces.dox_in"
 #include "internal_data.dox_in"

doxygen/users_guide/main_page.dox_in

@@ -78,7 +78,7 @@
 // section 5
 #include "S_main.dox_in"
 #include "input_file.dox_in"
-#include "sim_services/ExternalApplications/main_page.dox_in"
+#include "sim_services/ExternalApplications/docs/main_page.dox_in"
 #include "runtime_output.dox_in"
 
 // section 6
@@ -90,27 +90,27 @@
 
 // section 7
 #include "simulation_capabilities.dox_in"
-#include "sim_services/Executive/main_page.dox_in"
-#include "sim_services/InputProcessor/main_page.dox_in"
-#include "sim_services/EventManager/main_page.dox_in"
-#include "sim_services/RealtimeSync/main_page.dox_in"
-#include "sim_services/Clock/main_page.dox_in"
-#include "sim_services/Timer/main_page.dox_in"
-#include "sim_services/RealtimeInjector/main_page.dox_in"
-#include "sim_services/MonteCarlo/main_page.dox_in"
-#include "sim_services/MasterSlave/main_page.dox_in"
-#include "sim_services/DataRecord/main_page.dox_in"
-#include "sim_services/MemoryManagerWrapper/main_page.dox_in"
-#include "sim_services/MemoryManager/main_page.dox_in"
+#include "sim_services/Executive/docs/main_page.dox_in"
+#include "sim_services/InputProcessor/docs/main_page.dox_in"
+#include "sim_services/EventManager/docs/main_page.dox_in"
+#include "sim_services/RealtimeSync/docs/main_page.dox_in"
+#include "sim_services/Clock/docs/main_page.dox_in"
+#include "sim_services/Timer/docs/main_page.dox_in"
+#include "sim_services/RealtimeInjector/docs/main_page.dox_in"
+#include "sim_services/MonteCarlo/docs/main_page.dox_in"
+#include "sim_services/MasterSlave/docs/main_page.dox_in"
+#include "sim_services/DataRecord/docs/main_page.dox_in"
+//#include "sim_services/CheckPointRestart/docs/main_page.dox_in"
+#include "sim_services/MemoryManager/docs/main_page.dox_in"
 #include "sim_services/Integrator/main_page.dox_in"
-#include "sim_services/FrameLog/main_page.dox_in"
+#include "sim_services/FrameLog/docs/main_page.dox_in"
 #include "sim_services/DebugPause/main_page.dox_in"
-#include "sim_services/EchoJobs/main_page.dox_in"
-#include "sim_services/VariableServer/main_page.dox_in"
-#include "sim_services/Message/main_page.dox_in"
-#include "sim_services/CommandLineArguments/main_page.dox_in"
-#include "sim_services/Environment/main_page.dox_in"
-#include "sim_services/STL/main_page.dox_in"
+#include "sim_services/EchoJobs/docs/main_page.dox_in"
+#include "sim_services/VariableServer/docs/main_page.dox_in"
+#include "sim_services/Message/docs/main_page.dox_in"
+#include "sim_services/CommandLineArguments/docs/main_page.dox_in"
+#include "sim_services/Environment/docs/main_page.dox_in"
+#include "sim_services/STL/docs/main_page.dox_in"
 
 // section 8
 #include "simulation_utilities.dox_in"

trick_source/sim_services/ExternalApplications/docs/main_page.dox_in

@@ -5,7 +5,7 @@
  * Trick provides the following graphical user interfaces:
  */
 
-#include "sim_services/ExternalApplications/scp.dox_in"
+#include "sim_services/ExternalApplications/docs/scp.dox_in"
 
 /**
  * @page LEVEL2cont
@@ -13,7 +13,7 @@
  *   Send control commands to and view the status of a simulation.
  */
 
-#include "sim_services/ExternalApplications/tv.dox_in"
+#include "sim_services/ExternalApplications/docs/tv.dox_in"
 
 /**
  * @page LEVEL2cont
@@ -21,7 +21,7 @@
  *   Browse and modify a simulation's variables while it's running. Launch integrated strip charts.
  */
 
-#include "sim_services/ExternalApplications/mtv.dox_in"
+#include "sim_services/ExternalApplications/docs/mtv.dox_in"
 
 /**
  * @page LEVEL2cont
@@ -29,7 +29,7 @@
  *   Manage the events and malfunctions of a simulation.
  */
 
-#include "sim_services/ExternalApplications/mm.dox_in"
+#include "sim_services/ExternalApplications/docs/mm.dox_in"
 
 /**
  * @page LEVEL2cont