Change capitalization of FindOpenCL.cmake to match original file.

Turn on free energy plugin by default.
Better rule for when to default build OpenMM wrappers.
Several tweaks to advanced vs. non-advanced cmake variables.

CMakeLists.txt

@@ -184,7 +184,8 @@ ENDIF(NEED_QUOTES)
 SET(OPENMM_VERSION
     "${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}.${OPENMM_BUILD_VERSION}"
      CACHE STRING "This is the version of OpenMM which will be built." FORCE)
-
+# We don't actually use this version for anything yet
+MARK_AS_ADVANCED(OPENMM_VERSION)
 
 SET(SHARED_TARGET ${OPENMM_LIBRARY_NAME})
 SET(STATIC_TARGET ${OPENMM_LIBRARY_NAME}_static)
@@ -266,11 +267,11 @@ FIND_PROGRAM(GCCXML_PATH gccxml PATH
     /usr/local/bin
     "C:/Program Files/gccxml 0.9/bin"
 )
-IF(GCCXML_PATH AND Java_FOUND)
+IF(GCCXML_PATH AND JAVA_RUNTIME)
     SET(OPENMM_BUILD_API_WRAPPERS ON CACHE BOOL "Build wrappers for C and Fortran")
-ELSE(GCCXML_PATH AND Java_FOUND)
+ELSE(GCCXML_PATH AND JAVA_RUNTIME)
     SET(OPENMM_BUILD_API_WRAPPERS OFF CACHE BOOL "Build wrappers for C and Fortran")
-ENDIF(GCCXML_PATH AND Java_FOUND)
+ENDIF(GCCXML_PATH AND JAVA_RUNTIME)
 IF(OPENMM_BUILD_API_WRAPPERS)
     ADD_SUBDIRECTORY(wrappers)
     SET(SOURCE_FILES ${SOURCE_FILES} wrappers/OpenMMCWrapper.cpp  wrappers/OpenMMFortranWrapper.cpp)
@@ -296,6 +297,9 @@ IF(DL_LIBRARY)
   TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${DL_LIBRARY})
   TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${DL_LIBRARY})
 ENDIF(DL_LIBRARY)
+IF(WIN32)
+    MARK_AS_ADVANCED(DL_LIBRARY)
+ENDIF(WIN32)
 
 ADD_SUBDIRECTORY(platforms/reference/tests)
 
@@ -319,7 +323,7 @@ IF(OPENMM_BUILD_BROOK_LIB)
     ADD_SUBDIRECTORY(platforms/brook)
 ENDIF(OPENMM_BUILD_BROOK_LIB)
 
-FIND_PACKAGE(OPENCL QUIET)
+FIND_PACKAGE(OpenCL QUIET)
 IF(OPENCL_FOUND)
     SET(OPENMM_BUILD_OPENCL_LIB ON CACHE BOOL "Build OpenMMOpenCL library for Nvidia GPUs")
 ELSE(OPENCL_FOUND)
@@ -328,10 +332,12 @@ ENDIF(OPENCL_FOUND)
 IF(OPENMM_BUILD_OPENCL_LIB)
     ADD_SUBDIRECTORY(platforms/opencl)
 ENDIF(OPENMM_BUILD_OPENCL_LIB)
+MARK_AS_ADVANCED(CLEAR OPENCL_INCLUDE_DIR)
+MARK_AS_ADVANCED(CLEAR OPENCL_LIBRARY)
 
 # FreeEnergy plugin
 
-SET(OPENMM_BUILD_FREE_ENERGY_PLUGIN OFF CACHE BOOL "Build FreeEnergy plugin for Nvidia GPUs")
+SET(OPENMM_BUILD_FREE_ENERGY_PLUGIN ON CACHE BOOL "Build FreeEnergy plugin for Nvidia GPUs")
 SET(OPENMM_BUILD_FREE_ENERGY_PATH)
 IF(OPENMM_BUILD_FREE_ENERGY_PLUGIN)
    SET(OPENMM_BUILD_FREE_ENERGY_PATH ${CMAKE_CURRENT_SOURCE_DIR}/plugins/freeEnergy)
@@ -352,6 +358,7 @@ INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS})
 #
 # Allow automated build and dashboard.
 #
+# redundant INCLUDE(Dart) statement
 # INCLUDE (Dart)
 
 #IF (UNIX AND NOT CYGWIN AND NOT APPLE)