Rearrange Empirical as submodule

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "libs/backward-cpp"]
 	path = libs/backward-cpp
 	url = https://github.com/bombela/backward-cpp.git
+[submodule "libs/Empirical"]
+	path = libs/Empirical
+	url = https://github.com/devosoft/Empirical.git

.vscode/c_cpp_properties.json

@@ -5,7 +5,7 @@
             "defines": [],
             "cStandard": "c11",
             "browse": {
-                "path": [ "${workspaceFolder}", "${workspaceFolder}/avida-core/include/public", "${workspaceFolder}/avida-core/include/private", "${workspaceFolder}/../Empirical/source", "${workspaceFolder}/avida-core/include/public/avida/core/*" ],
+                "path": [ "${workspaceFolder}", "${workspaceFolder}/avida-core/include/public", "${workspaceFolder}/avida-core/include/private", "${workspaceFolder}/libs/Empirical/include/emp", "${workspaceFolder}/avida-core/include/public/avida/core/*" ],
                 "limitSymbolsToIncludedHeaders": true
             },
             "includePath": [
@@ -19,7 +19,7 @@
                 "${workspaceFolder}/avida-core/source/core",
                 "${workspaceFolder}/avida-core/source/actions",
                 "${workspaceFolder}/avida-core/source/script",
-                "${workspaceFolder}/../Empirical/source"
+                "${workspaceFolder}/libs/Empirical/include/emp"
             ]
         }
     ],

CMakeLists.txt

@@ -24,7 +24,7 @@ SET(LIBRARY_OUTPUT_PATH
   "Built libraries are placed here before installation."
 )
 
-INCLUDE_DIRECTORIES(../Empirical/include/emp)
+INCLUDE_DIRECTORIES(libs/Empirical/include/emp)
 
 ADD_SUBDIRECTORY(libs/apto)
 if(NOT WIN32 AND NOT DEFINED ENV{AVIDA_DISABLE_BACKTRACE})
@@ -34,7 +34,7 @@ IF(NOT WIN32)
   ADD_SUBDIRECTORY(libs/tcmalloc-1.4)
 ENDIF(NOT WIN32)
 ADD_SUBDIRECTORY(avida-core)
-# ADD_SUBDIRECTORY(../Empirical/include/emp .)
+# ADD_SUBDIRECTORY(libs/Empirical/include/emp .)
 
 # Default location for installed software/configs/ docs is the build directory.
 SET(CMAKE_INSTALL_PREFIX

README.md

@@ -1,7 +1,5 @@
 This is a version of Avida with the systematics tracker and open-ended evolution metrics from [Empirical](https://github.com/devosoft/Empirical).
-Specifically, it has been tested and is known to be compatible with [this release](https://github.com/emilydolson/Empirical/tree/OEE_metrics_paper_submission)
-of Empirical. The build file expects the directory containing that version of Empirical to be in the same directory as this
-repository (i.e. `ls` should show `Empirical` and `avida-empirical`).
+Empirical is managed as a submodule in this repository, pinned to a known-compatible commit.
 
 Other than that, this is the same as normal Avida. The README for normal Avida follows.