git: e14e1fc1a3eb - main - science/opensim-core: update 4.1 → 4.6

Yuri Victorovich <[email protected]> Sun, 02 Aug 2026 23:54:44 +0000
Newsgroups	gmane.os.freebsd.devel.cvs.ports
Message-ID	<[email protected]>
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=e14e1fc1a3ebfff180c0ae44c6f0944e83bd07af

commit e14e1fc1a3ebfff180c0ae44c6f0944e83bd07af
Author:     Thierry Thomas <[email protected]>
AuthorDate: 2026-08-02 23:43:43 +0000
Commit:     Yuri Victorovich <[email protected]>
CommitDate: 2026-08-02 23:54:24 +0000

    science/opensim-core: update 4.1 → 4.6
    
    PR:             297103
---
 science/opensim-core/Makefile                      |  38 +-
 science/opensim-core/distinfo                      |   6 +-
 .../patch-Applications_opensim-cmd_CMakeLists.txt  |  11 -
 science/opensim-core/files/patch-Bindings-common.i |  14 -
 science/opensim-core/files/patch-CMakeLists.txt    |  99 +++++-
 .../files/patch-OpenSim_Common_Array.h             |  12 +
 .../opensim-core/files/patch-OpenSim_Common_IO.cpp |  37 +-
 .../files/patch-OpenSim_Common_Logger.cpp          |  12 +
 .../files/patch-OpenSim_Common_Logger.h            |  14 +
 science/opensim-core/files/patch-buildWheel.cmake  |  10 +
 .../opensim-core/files/patch-cmake_CMakeLists.txt  |  11 +
 .../files/patch-cmake_OpenSimMacros.cmake          |  13 +
 ...SimMocoInstallLinuxDependencyLibraries.cmake.in |  33 ++
 science/opensim-core/pkg-plist                     | 389 +++++++++++++++++++--
 14 files changed, 582 insertions(+), 117 deletions(-)

diff --git a/science/opensim-core/Makefile b/science/opensim-core/Makefile
index 495d4f758a0c..5ebf9de47095 100644
--- a/science/opensim-core/Makefile
+++ b/science/opensim-core/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	OpenSim
-DISTVERSION=	4.1
-PORTREVISION=	12
+DISTVERSION=	4.6
 CATEGORIES=	science
 PKGNAMESUFFIX=	-core
 
@@ -11,45 +10,52 @@ WWW=		https://opensim.stanford.edu/
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-DEPRECATED=	Depends on expired devel/swig40
-EXPIRATION_DATE=2026-09-30
-
 BUILD_DEPENDS=	bash:shells/bash
-LIB_DEPENDS=	libdocopt.so:devel/docopt.cpp \
+LIB_DEPENDS=	libfmt.so:devel/libfmt \
+		libipopt.so:math/ipopt \
+		libcasadi.so:math/casadi \
+		libspdlog.so:devel/spdlog \
+		libdocopt.so:devel/docopt.cpp \
 		libSimTKcommon.so:science/simbody
+TEST_DEPENDS=	catch2>0:devel/catch2
 
-USES=		blaslapack:openblas cmake compiler:c++11-lib fortran gl shebangfix xorg # fortran only for simbody/openblas
+USES=		blaslapack:openblas cmake compiler:c++20-lang fortran gl pkgconfig shebangfix xorg # fortran only for simbody/openblas
 SHEBANG_FILES=	Applications/opensim-install-command-line.sh
 USE_GITHUB=	yes
 GH_ACCOUNT=	${PORTNAME:tl}-org
 GH_PROJECT=	${PORTNAME:tl}-core
 USE_GL=		gl glu glut
-JAVA_VERSION=	8
+JAVA_VERSION=	25
 USE_XORG=	xi xmu
 USE_LDCONFIG=	yes
 
+BINARY_ALIAS=	git=false
 CXXFLAGS+=	-I${LOCALBASE}/include/docopt
 CONFIGURE_ENV+=	SIMBODY_HOME=${LOCALBASE}
-CMAKE_OFF=	OPENSIM_COPY_DEPENDENCIES DO_TESTING
+CMAKE_OFF=	DO_TESTING
 
 OPTIONS_DEFINE=		PYTHON JAVA DOCS
 OPTIONS_DEFAULT=	PYTHON JAVA
 OPTIONS_SUB=		yes
 
 PYTHON_CMAKE_BOOL=	BUILD_PYTHON_WRAPPING
+PYTHON_CMAKE_OFF=	OPENSIM_COPY_DEPENDENCIES
 PYTHON_USES=		python
-PYTHON_BUILD_DEPENDS=	swig40:devel/swig40
-PYTHON_BINARY_ALIAS=	swig=swig40
+PYTHON_BUILD_DEPENDS=	swig:devel/swig \
+			${PYTHON_PKGNAMEPREFIX}numpy>0:math/py-numpy@${PY_FLAVOR}
+PYTHON_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}numpy>0:math/py-numpy@${PY_FLAVOR}
 
 JAVA_CMAKE_BOOL=	BUILD_JAVA_WRAPPING
-JAVA_CMAKE_ON=		-DJAVA_AWT_LIBRARY=${LOCALBASE}/openjdk8/jre/lib/amd64/libawt.so \
-			-DJAVA_JVM_LIBRARY=${LOCALBASE}/openjdk8/jre/lib/amd64/server/libjvm.so \
-			-DJAVA_INCLUDE_PATH=${LOCALBASE}/openjdk8/include
+JAVA_CMAKE_OFF=		OPENSIM_COPY_DEPENDENCIES
+JAVA_CMAKE_ON=		-DJAVA_AWT_LIBRARY=${JAVA_HOME}/lib/libawt.so \
+			-DJAVA_JVM_LIBRARY=${JAVA_HOME}/lib/server/libjvm.so \
+			-DJAVA_INCLUDE_PATH=${JAVA_HOME}/include
 JAVA_USES=		java
-JAVA_BUILD_DEPENDS=	swig40:devel/swig40
-JAVA_BINARY_ALIAS=	swig=swig40
+JAVA_BUILD_DEPENDS=	swig:devel/swig
 
+DOCS_BUILD_DEPENDS=	pdflatex:print/tex-formats
 DOCS_CMAKE_BOOL=	INSTALL_DOCS
+DOCS_CMAKE_OFF=		OPENSIM_DOXYGEN_USE_MATHJAX
 PORTDOCS=		*
 
 do-test: # 4 testcases are known to fail: https://github.com/opensim-org/opensim-core/issues/2379
diff --git a/science/opensim-core/distinfo b/science/opensim-core/distinfo
index c0c72f5b290d..37e33c2d8ebf 100644
--- a/science/opensim-core/distinfo
+++ b/science/opensim-core/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1580791628
-SHA256 (opensim-org-opensim-core-4.1_GH0.tar.gz) = 4cd301f6e2cf3a50af2491dd002f1701c33d89e4085fe7bb7dcfacc5c7c92691
-SIZE (opensim-org-opensim-core-4.1_GH0.tar.gz) = 47951542
+TIMESTAMP = 1785095678
+SHA256 (opensim-org-opensim-core-4.6_GH0.tar.gz) = 759ba196e6a744996fed3f19103bf0d2d9906d2233441f35ffbba231ceca7c21
+SIZE (opensim-org-opensim-core-4.6_GH0.tar.gz) = 43342662
diff --git a/science/opensim-core/files/patch-Applications_opensim-cmd_CMakeLists.txt b/science/opensim-core/files/patch-Applications_opensim-cmd_CMakeLists.txt
deleted file mode 100644
index bb103041fd46..000000000000
--- a/science/opensim-core/files/patch-Applications_opensim-cmd_CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
---- Applications/opensim-cmd/CMakeLists.txt.orig	2018-11-15 17:30:25 UTC
-+++ Applications/opensim-cmd/CMakeLists.txt
-@@ -20,7 +20,7 @@ OpenSimAddApplication(NAME opensim-cmd
-             parse_arguments.h
-     )
- 
--target_link_libraries(opensim-cmd docopt_s)
-+target_link_libraries(opensim-cmd docopt)
- 
- if(BUILD_TESTING)
-     subdirs(test)
diff --git a/science/opensim-core/files/patch-Bindings-common.i b/science/opensim-core/files/patch-Bindings-common.i
deleted file mode 100644
index 0a87dcf3dce2..000000000000
--- a/science/opensim-core/files/patch-Bindings-common.i
+++ /dev/null
@@ -1,14 +0,0 @@
---- Bindings/common.i.orig	2020-02-01 04:17:56 UTC
-+++ Bindings/common.i
-@@ -353,9 +353,11 @@ DATATABLE_CLONE(double, SimTK::Rotation_<double>)
- 
- %include <OpenSim/Common/Event.h>
- %template(StdVectorEvent) std::vector<OpenSim::Event>;
-+/*
- %template(StdMapStringTimeSeriesTableVec3)
-         std::map<std::string, 
-                  std::shared_ptr<OpenSim::TimeSeriesTable_<SimTK::Vec3>>>;
-+*/
- %shared_ptr(OpenSim::DataAdapter)
- %shared_ptr(OpenSim::FileAdapter)
- %shared_ptr(OpenSim::DelimFileAdapter)
diff --git a/science/opensim-core/files/patch-CMakeLists.txt b/science/opensim-core/files/patch-CMakeLists.txt
index 7a2988a5e0ed..0d6c3f17f7b2 100644
--- a/science/opensim-core/files/patch-CMakeLists.txt
+++ b/science/opensim-core/files/patch-CMakeLists.txt
@@ -1,6 +1,96 @@
---- CMakeLists.txt.orig	2018-11-12 23:49:48 UTC
+--- CMakeLists.txt.orig	2026-06-18 22:26:24 UTC
 +++ CMakeLists.txt
-@@ -766,8 +766,10 @@ endif(WIN32)
+@@ -789,13 +789,6 @@ if(OPENSIM_WITH_CASADI)
+     # Copy CasADi into our installation.
+     OpenSimCopyDependencyDLLsForWin(DEP_NAME casadi
+             DEP_BIN_DIR "${CASADI_BIN_DIR}")
+-    if(OPENSIM_COPY_DEPENDENCIES AND NOT WIN32)
+-        # OpenSimCopyDependencyDLLsForWin() only copies DLLs for Windows, but 
+-        # we still need the CasADi shared libraries on other platforms.
+-        install(DIRECTORY "${CASADI_CMAKE_DIR}/../../../"
+-            DESTINATION "${CMAKE_INSTALL_PREFIX}/${OPENSIM_INSTALL_CASADIDIR}"
+-                USE_SOURCE_PERMISSIONS)
+-    endif()
+ endif()
+ 
+ # IPOPT
+@@ -837,23 +830,6 @@ if (OPENSIM_WITH_CASADI)
+                 ${libquadmath_name}
+                 ${libgcc_name}
+                 DESTINATION ${CMAKE_INSTALL_LIBDIR})
+-        elseif(OPENSIM_COPY_DEPENDENCIES)
+-            get_filename_component(gcc_libdir "${pkgcfg_lib_IPOPT_gfortran}" DIRECTORY)
+-
+-            file(GLOB gfortran "${gcc_libdir}/../../../x86_64-linux-gnu/libgfortran*.so*")
+-            file(GLOB quadmath "${gcc_libdir}/../../../x86_64-linux-gnu/libquadmath*.so*")
+-
+-            install(FILES
+-                ${IPOPT_LIBDIR}/libipopt.so.3.14.16
+-                ${IPOPT_LIBDIR}/libipopt.so.3
+-                ${IPOPT_LIBDIR}/libipopt.so
+-                ${IPOPT_LIBDIR}/libcoinmumps.so.3.0.5
+-                ${IPOPT_LIBDIR}/libcoinmumps.so.3
+-                ${IPOPT_LIBDIR}/libcoinmumps.so
+-                ${IPOPT_LIBDIR}/libmetis.so
+-                ${gfortran}
+-                ${quadmath}
+-                DESTINATION ${CMAKE_INSTALL_LIBDIR})
+         endif()
+         if(BUILD_PYTHON_WRAPPING AND OPENSIM_PYTHON_STANDALONE)
+             OpenSimInstallDependencyLibraries(ipopt "${IPOPT_LIBDIR}"
+@@ -908,40 +884,6 @@ if(${OPENSIM_COPY_DEPENDENCIES})
+         # folders; we would prefer to only copy to the former, but
+         # SimbodyTargets-*.cmake expect dlls in sdk/Simbody/bin. In the future,
+         # we can edit the *.cmake files to no longer expect these DLLs.
+-    else()
+-        # We would have liked to use install(DIRECTORY) on UNIX, but the
+-        # dependencies may be installed in system-wide locations and we don't
+-        # want to copy extraneous files/directories; install(DIRECTORY) creates
+-        # a directory in DESTINATION for *every* directory in DIRECTORY, even
+-        # if we do not want to copy any files from some of the directories in
+-        # DIRECTORY.
+-
+-        # include
+-        file(RELATIVE_PATH install_simbodyincludedir
+-            "${Simbody_ROOT_DIR}" "${Simbody_INCLUDE_DIR}")
+-        install(DIRECTORY "${Simbody_INCLUDE_DIR}/"
+-                DESTINATION "${OPENSIM_INSTALL_SIMBODYDIR}/${install_simbodyincludedir}")
+-    
+-        # lib (and cmake, pkgconfig)
+-        file(RELATIVE_PATH install_simbodylibdir 
+-            "${Simbody_ROOT_DIR}/" "${Simbody_LIB_DIR}/")
+-        file(GLOB_RECURSE simbody_desired_lib_files
+-            RELATIVE "${Simbody_LIB_DIR}"
+-            "${Simbody_LIB_DIR}/*SimTK*" "${Simbody_LIB_DIR}/*Simbody*.cmake"
+-            "${Simbody_LIB_DIR}/*SampleCMakeLists.txt*")
+-        foreach(simbody_lib_file ${simbody_desired_lib_files})
+-            get_filename_component(subdir "${simbody_lib_file}" DIRECTORY)
+-            install(FILES "${Simbody_LIB_DIR}/${simbody_lib_file}"
+-                DESTINATION "${OPENSIM_INSTALL_SIMBODYDIR}/${install_simbodylibdir}/${subdir}")
+-        endforeach()
+-    
+-        # simbody-visualizer
+-        file(RELATIVE_PATH install_simbodyvizdir 
+-            "${Simbody_ROOT_DIR}" "${Simbody_VIZ_DIR}")
+-        install(DIRECTORY "${Simbody_VIZ_DIR}/"
+-                DESTINATION "${OPENSIM_INSTALL_SIMBODYDIR}/${install_simbodyvizdir}"
+-                USE_SOURCE_PERMISSIONS
+-                FILES_MATCHING PATTERN "*simbody-visualizer*")
+     endif()
+ 
+     # EZC3D
+@@ -953,10 +895,6 @@ if(${OPENSIM_COPY_DEPENDENCIES})
+                 DESTINATION "${CMAKE_INSTALL_LIBDIR}")
+     endif()
+ 
+-    # spdlog
+-    # ------
+-    install(DIRECTORY "${spdlog_DIR}/../../../"
+-            DESTINATION "${OPENSIM_INSTALL_SPDLOGDIR}")
+ endif()
+ 
+ if(BUILD_PYTHON_WRAPPING AND OPENSIM_PYTHON_STANDALONE)
+@@ -976,8 +914,10 @@ endif(WIN32)
  
  
  ## The following are required to uses Dart and the Cdash dashboard per Jesse
@@ -13,7 +103,7 @@
  
  # Sets the number of concurrent jobs that testing can use.
  if(MSVC OR XCODE)
-@@ -834,4 +836,6 @@ endif()
+@@ -1044,7 +984,9 @@ add_subdirectory(cmake)
  add_subdirectory(Bindings)
  
  add_subdirectory(cmake)
@@ -21,3 +111,6 @@
 +if (INSTALL_DOCS)
 +    add_subdirectory(doc)
 +endif()
+ 
+ # Print a list of the dependencies that were found, and the features the user
+ # chose.
diff --git a/science/opensim-core/files/patch-OpenSim_Common_Array.h b/science/opensim-core/files/patch-OpenSim_Common_Array.h
new file mode 100644
index 000000000000..403672edeada
--- /dev/null
+++ b/science/opensim-core/files/patch-OpenSim_Common_Array.h
@@ -0,0 +1,12 @@
+--- OpenSim/Common/Array.h.orig	2026-06-18 22:26:24 UTC
++++ OpenSim/Common/Array.h
+@@ -35,7 +35,8 @@
+ #include <initializer_list>
+ #include <iostream>
+ #include <iterator>
+-#include <spdlog/fmt/bundled/ostream.h>
++// On FreeBSD fmt is not bundled with spdlog
++#include <fmt/ostream.h>
+ #include <type_traits>
+ #include <utility>
+ #include <vector>
diff --git a/science/opensim-core/files/patch-OpenSim_Common_IO.cpp b/science/opensim-core/files/patch-OpenSim_Common_IO.cpp
index 67223730d0c3..4ea73ad9b90a 100644
--- a/science/opensim-core/files/patch-OpenSim_Common_IO.cpp
+++ b/science/opensim-core/files/patch-OpenSim_Common_IO.cpp
@@ -1,38 +1,11 @@
---- OpenSim/Common/IO.cpp.orig	2018-11-15 09:02:08 UTC
+--- OpenSim/Common/IO.cpp.orig	2026-06-18 22:26:24 UTC
 +++ OpenSim/Common/IO.cpp
-@@ -33,7 +33,7 @@
- #include <climits>
- 
- #include "IO.h"
+@@ -37,7 +37,7 @@
+ #include <string>
+ #include <sstream>
+ #include <time.h>
 -#if defined(__linux__) || defined(__APPLE__)
 +#if defined(__linux__) || defined(__APPLE__) || defined(__FreeBSD__)
      #include <sys/stat.h>
      #include <sys/types.h>
  #elif defined(_MSC_VER)
-@@ -476,7 +476,7 @@ int IO::
- makeDir(const string &aDirName)
- {
- 
--#if defined __linux__ || defined __APPLE__
-+#if defined __linux__ || defined __APPLE__ || defined __FreeBSD__
-     return mkdir(aDirName.c_str(),S_IRWXU);
- #else
-     return _mkdir(aDirName.c_str());
-@@ -491,7 +491,7 @@ int IO::
- chDir(const string &aDirName)
- {
- 
--#if defined __linux__ || defined __APPLE__
-+#if defined __linux__ || defined __APPLE__ || defined __FreeBSD__
-     return chdir(aDirName.c_str()); 
- #else
-     return _chdir(aDirName.c_str());
-@@ -507,7 +507,7 @@ string IO::
- getCwd()
- {
-     char buffer[PATH_MAX];
--#if defined __linux__ || defined __APPLE__
-+#if defined __linux__ || defined __APPLE__ || defined __FreeBSD__
-     auto ptr = getcwd(buffer, PATH_MAX); (void)ptr;
- #else
-     _getcwd(buffer, PATH_MAX);
diff --git a/science/opensim-core/files/patch-OpenSim_Common_Logger.cpp b/science/opensim-core/files/patch-OpenSim_Common_Logger.cpp
new file mode 100644
index 000000000000..be6195b12437
--- /dev/null
+++ b/science/opensim-core/files/patch-OpenSim_Common_Logger.cpp
@@ -0,0 +1,12 @@
+--- OpenSim/Common/Logger.cpp.orig	2026-06-18 22:26:24 UTC
++++ OpenSim/Common/Logger.cpp
+@@ -26,7 +26,8 @@
+ #include "IO.h"                              // for IO
+ #include "LogSink.h"                         // for LogSink
+ #include <algorithm>                         // for remove
+-#include <spdlog/fmt/bundled/format.h>       // for format
++// On FreeBSD fmt is not bundled with spdlog
++#include <fmt/format.h>       // for format
+ #include <spdlog/sinks/basic_file_sink.h>    // for basic_file_sink_mt, bas...
+ #include <spdlog/sinks/sink.h>               // for sink
+ #include <spdlog/sinks/stdout_color_sinks.h> // for stdout_color_mt
diff --git a/science/opensim-core/files/patch-OpenSim_Common_Logger.h b/science/opensim-core/files/patch-OpenSim_Common_Logger.h
new file mode 100644
index 000000000000..489f789b7303
--- /dev/null
+++ b/science/opensim-core/files/patch-OpenSim_Common_Logger.h
@@ -0,0 +1,14 @@
+--- OpenSim/Common/Logger.h.orig	2026-06-18 22:26:24 UTC
++++ OpenSim/Common/Logger.h
+@@ -25,8 +25,9 @@
+ #include "osimCommonDLL.h"              // for OSIMCOMMON_API
+ #include <memory>                       // for shared_ptr
+ #include <spdlog/common.h>              // for spdlog::format_string_t
+-#include <spdlog/fmt/bundled/base.h>    // for formatter
+-#include <spdlog/fmt/bundled/ostream.h> // for ostream_formatter
++// On FreeBSD fmt is not bundled with spdlog
++#include <fmt/base.h>    // for formatter
++#include <fmt/ostream.h> // for ostream_formatter
+ #include <spdlog/logger.h>              // for logger
+ #include <string>                       // for basic_string, string
+ #include <string_view>                  // for std::string_view
diff --git a/science/opensim-core/files/patch-buildWheel.cmake b/science/opensim-core/files/patch-buildWheel.cmake
new file mode 100644
index 000000000000..7fb2b81ed0d2
--- /dev/null
+++ b/science/opensim-core/files/patch-buildWheel.cmake
@@ -0,0 +1,10 @@
+--- buildWheel.cmake.orig	2026-06-18 22:26:24 UTC
++++ buildWheel.cmake
+@@ -22,6 +22,6 @@ else()
+     # add $ORIGIN to rpath as layout has changed
+     file(GLOB SIMTK_LIBS "${CMAKE_INSTALL_PREFIX}/${OPENSIM_INSTALL_PYTHONDIR}/opensim/libSimTK*.so*")
+     foreach(slib ${SIMTK_LIBS})
+-        execute_process(COMMAND bash "-c" "patchelf --force-rpath --set-rpath '$ORIGIN' '${slib}'")
++        #execute_process(COMMAND bash "-c" "patchelf --force-rpath --set-rpath '$ORIGIN' '${slib}'")
+     endforeach()
+ endif()
diff --git a/science/opensim-core/files/patch-cmake_CMakeLists.txt b/science/opensim-core/files/patch-cmake_CMakeLists.txt
new file mode 100644
index 000000000000..494eaaa5b6c3
--- /dev/null
+++ b/science/opensim-core/files/patch-cmake_CMakeLists.txt
@@ -0,0 +1,11 @@
+--- cmake/CMakeLists.txt.orig	2026-06-18 22:26:24 UTC
++++ cmake/CMakeLists.txt
+@@ -59,7 +59,7 @@ if(UNIX AND OPENSIM_COPY_DEPENDENCIES AND OPENSIM_WITH
+     # is installed (add_subdirectory(cmake) must be after
+     # add_subdirectory(Moco)).
+     if (OPENSIM_WITH_CASADI)
+-        get_target_property(CASADI_LIBRARY_LOCATION casadi LOCATION)
++        get_target_property(CASADI_LIBRARY_LOCATION casadi::casadi LOCATION)
+         get_filename_component(CASADI_LIBDIR "${CASADI_LIBRARY_LOCATION}" DIRECTORY)
+     endif()
+ 
diff --git a/science/opensim-core/files/patch-cmake_OpenSimMacros.cmake b/science/opensim-core/files/patch-cmake_OpenSimMacros.cmake
new file mode 100644
index 000000000000..6c9f6e944169
--- /dev/null
+++ b/science/opensim-core/files/patch-cmake_OpenSimMacros.cmake
@@ -0,0 +1,13 @@
+--- cmake/OpenSimMacros.cmake.orig	2026-06-18 22:26:24 UTC
++++ cmake/OpenSimMacros.cmake
+@@ -619,8 +619,8 @@ function(OpenSimInstallVisualizer DEP_LIBS_DIR_WIN
+             set(simbody_visualizer "${DEP_LIBS_DIR_UNIX}/../libexec/simbody/simbody-visualizer")
+             install(FILES ${simbody_visualizer} DESTINATION "${OSIM_DESTINATION}")
+             # On Linux, the visualizer is a dynamically linked executable, we need fix rpath
+-            execute_process(COMMAND bash "-c" "patchelf --set-rpath '$ORIGIN/:$ORIGIN/../../lib' '${simbody_visualizer}'" OUTPUT_VARIABLE res)
+-            message(STATUS "patchelf --set-rpath '$ORIGIN/:.$ORIGIN/../../lib' '${simbody_visualizer}' '${res}'")
++            #execute_process(COMMAND bash "-c" "patchelf --set-rpath '$ORIGIN/:$ORIGIN/../../lib' '${simbody_visualizer}'" OUTPUT_VARIABLE res)
++            #message(STATUS "patchelf --set-rpath '$ORIGIN/:.$ORIGIN/../../lib' '${simbody_visualizer}' '${res}'")
+         endif()
+     endif()
+ endfunction()
diff --git a/science/opensim-core/files/patch-cmake_OpenSimMocoInstallLinuxDependencyLibraries.cmake.in b/science/opensim-core/files/patch-cmake_OpenSimMocoInstallLinuxDependencyLibraries.cmake.in
new file mode 100644
index 000000000000..0aef7ea2229a
--- /dev/null
+++ b/science/opensim-core/files/patch-cmake_OpenSimMocoInstallLinuxDependencyLibraries.cmake.in
@@ -0,0 +1,33 @@
+--- cmake/OpenSimMocoInstallLinuxDependencyLibraries.cmake.in.orig	2026-06-18 22:26:24 UTC
++++ cmake/OpenSimMocoInstallLinuxDependencyLibraries.cmake.in
+@@ -6,21 +6,21 @@ macro(install_name_tool_add_rpath lib)
+ set(libdir "@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@")
+ 
+ macro(install_name_tool_add_rpath lib)
+-    execute_process(COMMAND bash "-c" "patchelf --force-rpath --set-rpath '$ORIGIN/:$ORIGIN/../../sdk/Simbody/lib' '${libdir}/lib${lib}'"
+-        OUTPUT_VARIABLE res)
+-    message(STATUS "patchelf --set-rpath '$ORIGIN/:../../sdk/Simbody/lib' '${libdir}/lib${lib}' '${res}'")
++    #execute_process(COMMAND bash "-c" "patchelf --force-rpath --set-rpath '$ORIGIN/:$ORIGIN/../../sdk/Simbody/lib' '${libdir}/lib${lib}'"
++    #    OUTPUT_VARIABLE res)
++    #message(STATUS "patchelf --set-rpath '$ORIGIN/:../../sdk/Simbody/lib' '${libdir}/lib${lib}' '${res}'")
+ endmacro()
+ 
+ macro(install_name_tool_delete_rpath lib)
+-    execute_process(COMMAND bash "-c" "patchelf --remove-rpath '${libdir}/lib${lib}'"
+-        OUTPUT_VARIABLE res)
+-    message(STATUS "patchelf --remove-rpath '${libdir}/lib${lib}' '${res}'")
++    #execute_process(COMMAND bash "-c" "patchelf --remove-rpath '${libdir}/lib${lib}'"
++    #    OUTPUT_VARIABLE res)
++    #message(STATUS "patchelf --remove-rpath '${libdir}/lib${lib}' '${res}'")
+ endmacro()
+ 
+ macro(install_name_tool_print_rpath lib)
+-    execute_process(COMMAND bash "-c" "patchelf --print-rpath '${libdir}/lib${lib}'"
+-        OUTPUT_VARIABLE created_rpath)
+-    message(STATUS "RPATH = '${created_rpath}'")
++    #execute_process(COMMAND bash "-c" "patchelf --print-rpath '${libdir}/lib${lib}'"
++    #    OUTPUT_VARIABLE created_rpath)
++    #message(STATUS "RPATH = '${created_rpath}'")
+ endmacro()
+ 
+ if (OPENSIM_WITH_CASADI)
diff --git a/science/opensim-core/pkg-plist b/science/opensim-core/pkg-plist
index 326cb4948a37..64ddc1e04880 100644
--- a/science/opensim-core/pkg-plist
+++ b/science/opensim-core/pkg-plist
@@ -2,11 +2,13 @@ bin/opensense
 bin/opensim-cmd
 bin/opensim-install-command-line.sh
 %%ETCDIR%%_buildinfo.txt
+include/OpenSim/Actuators/ActivationCoordinateActuator.h
 include/OpenSim/Actuators/ActiveForceLengthCurve.h
 include/OpenSim/Actuators/BodyActuator.h
 include/OpenSim/Actuators/ClutchedPathSpring.h
 include/OpenSim/Actuators/ConstantMuscleActivation.h
 include/OpenSim/Actuators/CoordinateActuator.h
+include/OpenSim/Actuators/DeGrooteFregly2016Muscle.h
 include/OpenSim/Actuators/Delp1990Muscle_Deprecated.h
 include/OpenSim/Actuators/FiberCompressiveForceCosPennationCurve.h
 include/OpenSim/Actuators/FiberCompressiveForceLengthCurve.h
@@ -15,14 +17,19 @@ include/OpenSim/Actuators/FirstOrderMuscleActivationDynamics.h
 include/OpenSim/Actuators/ForceVelocityCurve.h
 include/OpenSim/Actuators/ForceVelocityInverseCurve.h
 include/OpenSim/Actuators/McKibbenActuator.h
+include/OpenSim/Actuators/MeyerFregly2016Muscle.h
 include/OpenSim/Actuators/Millard2012AccelerationMuscle.h
 include/OpenSim/Actuators/Millard2012EquilibriumMuscle.h
+include/OpenSim/Actuators/ModelFactory.h
+include/OpenSim/Actuators/ModelOperators.h
+include/OpenSim/Actuators/ModelProcessor.h
 include/OpenSim/Actuators/MuscleActivationDynamics.h
 include/OpenSim/Actuators/MuscleFirstOrderActivationDynamicModel.h
 include/OpenSim/Actuators/MuscleFixedWidthPennationModel.h
 include/OpenSim/Actuators/MuscleSecondOrderActivationDynamicModel.h
 include/OpenSim/Actuators/PointActuator.h
 include/OpenSim/Actuators/PointToPointActuator.h
+include/OpenSim/Actuators/PolynomialPathFitter.h
 include/OpenSim/Actuators/RegisterTypes_osimActuators.h
 include/OpenSim/Actuators/RigidTendonMuscle.h
 include/OpenSim/Actuators/Schutte1993Muscle_Deprecated.h
@@ -37,6 +44,7 @@ include/OpenSim/Actuators/osimActuatorsDLL.h
 include/OpenSim/Analyses/Actuation.h
 include/OpenSim/Analyses/BodyKinematics.h
 include/OpenSim/Analyses/ForceReporter.h
+include/OpenSim/Analyses/IMUDataReporter.h
 include/OpenSim/Analyses/InducedAccelerations.h
 include/OpenSim/Analyses/InducedAccelerationsSolver.h
 include/OpenSim/Analyses/InverseDynamics.h
@@ -60,6 +68,7 @@ include/OpenSim/Common/AbstractProperty.h
 include/OpenSim/Common/Adapters.h
 include/OpenSim/Common/Array.h
 include/OpenSim/Common/ArrayPtrs.h
+include/OpenSim/Common/Assertion.h
 include/OpenSim/Common/CSVFileAdapter.h
 include/OpenSim/Common/CommonUtilities.h
 include/OpenSim/Common/Component.h
@@ -69,12 +78,14 @@ include/OpenSim/Common/ComponentPath.h
 include/OpenSim/Common/ComponentSocket.h
 include/OpenSim/Common/Constant.h
 include/OpenSim/Common/DataAdapter.h
+include/OpenSim/Common/DataQueue.h
 include/OpenSim/Common/DataTable.h
 include/OpenSim/Common/DebugUtilities.h
 include/OpenSim/Common/DelimFileAdapter.h
 include/OpenSim/Common/Event.h
 include/OpenSim/Common/Exception.h
 include/OpenSim/Common/ExperimentalSensor.h
+include/OpenSim/Common/ExpressionBasedFunction.h
 include/OpenSim/Common/FileAdapter.h
 include/OpenSim/Common/Function.h
 include/OpenSim/Common/FunctionAdapter.h
@@ -83,20 +94,20 @@ include/OpenSim/Common/GCVSpline.h
 include/OpenSim/Common/GCVSplineSet.h
 include/OpenSim/Common/IMUDataReader.h
 include/OpenSim/Common/IO.h
+include/OpenSim/Common/LatinHypercubeDesign.h
 include/OpenSim/Common/LinearFunction.h
 include/OpenSim/Common/Lmdif.h
 include/OpenSim/Common/LoadOpenSimLibrary.h
-include/OpenSim/Common/LogCallback.h
-include/OpenSim/Common/LogManager.h
+include/OpenSim/Common/LogSink.h
+include/OpenSim/Common/Logger.h
 include/OpenSim/Common/MarkerData.h
 include/OpenSim/Common/MarkerFrame.h
 include/OpenSim/Common/ModelDisplayHints.h
-include/OpenSim/Common/Mtx.h
 include/OpenSim/Common/MultiplierFunction.h
+include/OpenSim/Common/MultivariatePolynomialFunction.h
 include/OpenSim/Common/Object.h
 include/OpenSim/Common/ObjectGroup.h
 include/OpenSim/Common/OptimizationTarget.h
-include/OpenSim/Common/Path.h
 include/OpenSim/Common/PiecewiseConstantFunction.h
 include/OpenSim/Common/PiecewiseLinearFunction.h
 include/OpenSim/Common/PolynomialFunction.h
@@ -124,6 +135,7 @@ include/OpenSim/Common/RootSolver.h
 include/OpenSim/Common/STOFileAdapter.h
 include/OpenSim/Common/Scale.h
 include/OpenSim/Common/ScaleSet.h
+include/OpenSim/Common/ScopeExit.h
 include/OpenSim/Common/SegmentedQuinticBezierToolkit.h
 include/OpenSim/Common/Set.h
 include/OpenSim/Common/Signal.h
@@ -142,6 +154,7 @@ include/OpenSim/Common/StorageFactory.h
 include/OpenSim/Common/StorageInterface.h
 include/OpenSim/Common/TRCFileAdapter.h
 include/OpenSim/Common/TableSource.h
+include/OpenSim/Common/TableUtilities.h
 include/OpenSim/Common/TimeSeriesTable.h
 include/OpenSim/Common/Units.h
 include/OpenSim/Common/ValueArray.h
@@ -162,8 +175,76 @@ include/OpenSim/ExampleComponents/ToyPropMyoController.h
 include/OpenSim/ExampleComponents/ToyReflexController.h
 include/OpenSim/ExampleComponents/osimExampleComponentsDLL.h
 include/OpenSim/Lepton.h
+include/OpenSim/Moco/About.h
+include/OpenSim/Moco/Components/AccelerationMotion.h
+include/OpenSim/Moco/Components/ActuatorInputController.h
+include/OpenSim/Moco/Components/ControlDistributor.h
+include/OpenSim/Moco/Components/DiscreteForces.h
+include/OpenSim/Moco/MocoBounds.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCFunction.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCHermiteSimpson.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCIterate.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCLegendreGauss.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCLegendreGaussRadau.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCProblem.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCSolver.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCTranscription.h
+include/OpenSim/Moco/MocoCasADiSolver/CasOCTrapezoidal.h
+include/OpenSim/Moco/MocoCasADiSolver/MocoCasADiSolver.h
+include/OpenSim/Moco/MocoCasADiSolver/MocoCasOCProblem.h
+include/OpenSim/Moco/MocoConstraint.h
+include/OpenSim/Moco/MocoConstraintInfo.h
+include/OpenSim/Moco/MocoControlBoundConstraint.h
+include/OpenSim/Moco/MocoDirectCollocationSolver.h
+include/OpenSim/Moco/MocoFrameDistanceConstraint.h
+include/OpenSim/Moco/MocoGoal/MocoAccelerationTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoAngularVelocityTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoContactImpulseTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoContactTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoControlGoal.h
+include/OpenSim/Moco/MocoGoal/MocoControlTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoExpressionBasedParameterGoal.h
+include/OpenSim/Moco/MocoGoal/MocoGeneralizedForceTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoGoal.h
+include/OpenSim/Moco/MocoGoal/MocoInitialActivationGoal.h
+include/OpenSim/Moco/MocoGoal/MocoInitialForceEquilibriumDGFGoal.h
+include/OpenSim/Moco/MocoGoal/MocoInitialVelocityEquilibriumDGFGoal.h
+include/OpenSim/Moco/MocoGoal/MocoJointReactionGoal.h
+include/OpenSim/Moco/MocoGoal/MocoMarkerFinalGoal.h
+include/OpenSim/Moco/MocoGoal/MocoMarkerTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoOrientationTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoOutputGoal.h
+include/OpenSim/Moco/MocoGoal/MocoPeriodicityGoal.h
+include/OpenSim/Moco/MocoGoal/MocoStateTrackingGoal.h
+include/OpenSim/Moco/MocoGoal/MocoStepLengthAsymmetryGoal.h
+include/OpenSim/Moco/MocoGoal/MocoStepTimeAsymmetryGoal.h
+include/OpenSim/Moco/MocoGoal/MocoSumSquaredStateGoal.h
+include/OpenSim/Moco/MocoGoal/MocoTranslationTrackingGoal.h
+include/OpenSim/Moco/MocoInverse.h
+include/OpenSim/Moco/MocoOutputBoundConstraint.h
+include/OpenSim/Moco/MocoOutputConstraint.h
+include/OpenSim/Moco/MocoParameter.h
+include/OpenSim/Moco/MocoProblem.h
+include/OpenSim/Moco/MocoProblemInfo.h
+include/OpenSim/Moco/MocoProblemRep.h
+include/OpenSim/Moco/MocoScaleFactor.h
+include/OpenSim/Moco/MocoSolver.h
+include/OpenSim/Moco/MocoStateBoundConstraint.h
+include/OpenSim/Moco/MocoStudy.h
+include/OpenSim/Moco/MocoStudyFactory.h
+include/OpenSim/Moco/MocoTool.h
+include/OpenSim/Moco/MocoTrack.h
+include/OpenSim/Moco/MocoTrajectory.h
+include/OpenSim/Moco/MocoUtilities.h
+include/OpenSim/Moco/MocoVariableInfo.h
+include/OpenSim/Moco/MocoWeightSet.h
+include/OpenSim/Moco/ModelOperatorsDGF.h
+include/OpenSim/Moco/RegisterTypes_osimMoco.h
+include/OpenSim/Moco/osimMoco.h
+include/OpenSim/Moco/osimMocoDLL.h
 include/OpenSim/OpenSim.h
 include/OpenSim/Simulation/AssemblySolver.h
+include/OpenSim/Simulation/BufferedOrientationsReference.h
 include/OpenSim/Simulation/Control/Control.h
 include/OpenSim/Simulation/Control/ControlConstant.h
 include/OpenSim/Simulation/Control/ControlLinear.h
@@ -171,13 +252,16 @@ include/OpenSim/Simulation/Control/ControlLinearNode.h
 include/OpenSim/Simulation/Control/ControlSet.h
 include/OpenSim/Simulation/Control/ControlSetController.h
 include/OpenSim/Simulation/Control/Controller.h
+include/OpenSim/Simulation/Control/InputController.h
 include/OpenSim/Simulation/Control/PrescribedController.h
+include/OpenSim/Simulation/Control/SynergyController.h
 include/OpenSim/Simulation/Control/TrackingController.h
 include/OpenSim/Simulation/CoordinateReference.h
 include/OpenSim/Simulation/InverseDynamicsSolver.h
 include/OpenSim/Simulation/InverseKinematicsSolver.h
 include/OpenSim/Simulation/Manager/Manager.h
 include/OpenSim/Simulation/MarkersReference.h
+include/OpenSim/Simulation/Model/AbstractGeometryPath.h
 include/OpenSim/Simulation/Model/AbstractPathPoint.h
 include/OpenSim/Simulation/Model/AbstractTool.h
 include/OpenSim/Simulation/Model/ActivationFiberLengthMuscle.h
@@ -189,6 +273,8 @@ include/OpenSim/Simulation/Model/Analysis.h
 include/OpenSim/Simulation/Model/AnalysisSet.h
 include/OpenSim/Simulation/Model/Appearance.h
 include/OpenSim/Simulation/Model/Bhargava2004MuscleMetabolicsProbe.h
+include/OpenSim/Simulation/Model/Bhargava2004SmoothedMuscleMetabolics.h
+include/OpenSim/Simulation/Model/Blankevoort1991Ligament.h
 include/OpenSim/Simulation/Model/BodyScale.h
 include/OpenSim/Simulation/Model/BodyScaleSet.h
 include/OpenSim/Simulation/Model/BodySet.h
@@ -202,21 +288,26 @@ include/OpenSim/Simulation/Model/ContactGeometry.h
 include/OpenSim/Simulation/Model/ContactGeometrySet.h
 include/OpenSim/Simulation/Model/ContactHalfSpace.h
 include/OpenSim/Simulation/Model/ContactMesh.h
-include/OpenSim/Simulation/Model/ContactSphere.h
 include/OpenSim/Simulation/Model/ControllerSet.h
 include/OpenSim/Simulation/Model/CoordinateLimitForce.h
 include/OpenSim/Simulation/Model/CoordinateSet.h
 include/OpenSim/Simulation/Model/ElasticFoundationForce.h
+include/OpenSim/Simulation/Model/ExponentialContactForce.h
 include/OpenSim/Simulation/Model/ExpressionBasedBushingForce.h
 include/OpenSim/Simulation/Model/ExpressionBasedCoordinateForce.h
+include/OpenSim/Simulation/Model/ExpressionBasedPathForce.h
 include/OpenSim/Simulation/Model/ExpressionBasedPointToPointForce.h
 include/OpenSim/Simulation/Model/ExternalForce.h
 include/OpenSim/Simulation/Model/ExternalLoads.h
 include/OpenSim/Simulation/Model/Force.h
 include/OpenSim/Simulation/Model/ForceAdapter.h
+include/OpenSim/Simulation/Model/ForceApplier.h
+include/OpenSim/Simulation/Model/ForceConsumer.h
+include/OpenSim/Simulation/Model/ForceProducer.h
 include/OpenSim/Simulation/Model/ForceSet.h
 include/OpenSim/Simulation/Model/Frame.h
 include/OpenSim/Simulation/Model/FunctionBasedBushingForce.h
+include/OpenSim/Simulation/Model/FunctionBasedPath.h
 include/OpenSim/Simulation/Model/FunctionThresholdCondition.h
 include/OpenSim/Simulation/Model/Geometry.h
 include/OpenSim/Simulation/Model/GeometryPath.h
@@ -227,6 +318,7 @@ include/OpenSim/Simulation/Model/JointSet.h
 include/OpenSim/Simulation/Model/Ligament.h
 include/OpenSim/Simulation/Model/Marker.h
 include/OpenSim/Simulation/Model/MarkerSet.h
+include/OpenSim/Simulation/Model/MeyerFregly2016Force.h
 include/OpenSim/Simulation/Model/Model.h
 include/OpenSim/Simulation/Model/ModelComponent.h
 include/OpenSim/Simulation/Model/ModelComponentSet.h
@@ -248,21 +340,26 @@ include/OpenSim/Simulation/Model/PointToPointSpring.h
 include/OpenSim/Simulation/Model/PrescribedForce.h
 include/OpenSim/Simulation/Model/Probe.h
 include/OpenSim/Simulation/Model/ProbeSet.h
+include/OpenSim/Simulation/Model/Scholz2015GeometryPath.h
+include/OpenSim/Simulation/Model/SmoothSphereHalfSpaceForce.h
 include/OpenSim/Simulation/Model/Station.h
+include/OpenSim/Simulation/Model/StationDefinedFrame.h
 include/OpenSim/Simulation/Model/SystemEnergyProbe.h
 include/OpenSim/Simulation/Model/TwoFrameLinker.h
 include/OpenSim/Simulation/Model/Umberger2010MuscleMetabolicsProbe.h
 include/OpenSim/Simulation/MomentArmSolver.h
 include/OpenSim/Simulation/OpenSense/ExperimentalFrame.h
 include/OpenSim/Simulation/OpenSense/ExperimentalMarker.h
-include/OpenSim/Simulation/OpenSense/IMUInverseKinematicsTool.h
+include/OpenSim/Simulation/OpenSense/IMU.h
 include/OpenSim/Simulation/OpenSense/IMUPlacer.h
 include/OpenSim/Simulation/OpenSense/OpenSenseUtilities.h
 include/OpenSim/Simulation/OrientationsReference.h
+include/OpenSim/Simulation/PositionMotion.h
 include/OpenSim/Simulation/Reference.h
 include/OpenSim/Simulation/RegisterTypes_osimSimulation.h
 include/OpenSim/Simulation/SimbodyEngine/BallJoint.h
 include/OpenSim/Simulation/SimbodyEngine/Body.h
+include/OpenSim/Simulation/SimbodyEngine/ConstantCurvatureJoint.h
 include/OpenSim/Simulation/SimbodyEngine/ConstantDistanceConstraint.h
 include/OpenSim/Simulation/SimbodyEngine/Constraint.h
 include/OpenSim/Simulation/SimbodyEngine/Coordinate.h
@@ -277,6 +374,7 @@ include/OpenSim/Simulation/SimbodyEngine/PlanarJoint.h
 include/OpenSim/Simulation/SimbodyEngine/PointConstraint.h
 include/OpenSim/Simulation/SimbodyEngine/PointOnLineConstraint.h
 include/OpenSim/Simulation/SimbodyEngine/RollingOnSurfaceConstraint.h
+include/OpenSim/Simulation/SimbodyEngine/ScapulothoracicJoint.h
 include/OpenSim/Simulation/SimbodyEngine/SimbodyEngine.h
 include/OpenSim/Simulation/SimbodyEngine/SliderJoint.h
 include/OpenSim/Simulation/SimbodyEngine/SpatialTransform.h
@@ -287,21 +385,21 @@ include/OpenSim/Simulation/SimbodyEngine/WeldConstraint.h
 include/OpenSim/Simulation/SimbodyEngine/WeldJoint.h
 include/OpenSim/Simulation/SimulationUtilities.h
 include/OpenSim/Simulation/Solver.h
+include/OpenSim/Simulation/StatesDocument.h
 include/OpenSim/Simulation/StatesTrajectory.h
 include/OpenSim/Simulation/StatesTrajectoryReporter.h
+include/OpenSim/Simulation/TableProcessor.h
+include/OpenSim/Simulation/VisualizerUtilities.h
 include/OpenSim/Simulation/Wrap/PathWrap.h
 include/OpenSim/Simulation/Wrap/PathWrapPoint.h
 include/OpenSim/Simulation/Wrap/PathWrapSet.h
 include/OpenSim/Simulation/Wrap/WrapCylinder.h
-include/OpenSim/Simulation/Wrap/WrapCylinderObst.h
-include/OpenSim/Simulation/Wrap/WrapDoubleCylinderObst.h
 include/OpenSim/Simulation/Wrap/WrapEllipsoid.h
 include/OpenSim/Simulation/Wrap/WrapMath.h
 include/OpenSim/Simulation/Wrap/WrapObject.h
 include/OpenSim/Simulation/Wrap/WrapObjectSet.h
 include/OpenSim/Simulation/Wrap/WrapResult.h
 include/OpenSim/Simulation/Wrap/WrapSphere.h
-include/OpenSim/Simulation/Wrap/WrapSphereObst.h
 include/OpenSim/Simulation/Wrap/WrapTorus.h
 include/OpenSim/Simulation/osimSimulation.h
 include/OpenSim/Simulation/osimSimulationDLL.h
@@ -323,8 +421,10 @@ include/OpenSim/Tools/IKCoordinateTask.h
 include/OpenSim/Tools/IKMarkerTask.h
 include/OpenSim/Tools/IKTask.h
 include/OpenSim/Tools/IKTaskSet.h
+include/OpenSim/Tools/IMUInverseKinematicsTool.h
 include/OpenSim/Tools/InverseDynamicsTool.h
 include/OpenSim/Tools/InverseKinematicsTool.h
+include/OpenSim/Tools/InverseKinematicsToolBase.h
 include/OpenSim/Tools/MarkerPair.h
 include/OpenSim/Tools/MarkerPairSet.h
 include/OpenSim/Tools/MarkerPlacer.h
@@ -342,6 +442,10 @@ include/OpenSim/Tools/TrackingTask.h
 include/OpenSim/Tools/VectorFunctionForActuators.h
 include/OpenSim/Tools/osimTools.h
 include/OpenSim/Tools/osimToolsDLL.h
+include/OpenSim/docopt/docopt.h
+include/OpenSim/docopt/docopt_private.h
+include/OpenSim/docopt/docopt_util.h
+include/OpenSim/docopt/docopt_value.h
 include/OpenSim/lepton/CompiledExpression.h
 include/OpenSim/lepton/CustomFunction.h
 include/OpenSim/lepton/Exception.h
@@ -356,19 +460,24 @@ lib/cmake/OpenSim/OpenSimConfigVersion.cmake
 lib/cmake/OpenSim/OpenSimTargets-%%CMAKE_BUILD_TYPE%%.cmake
 lib/cmake/OpenSim/OpenSimTargets.cmake
 lib/cmake/OpenSim/SampleCMakeLists.txt
+lib/cmake/OpenSim/UseOpenSim.cmake
 lib/libosimActuators.so
 lib/libosimAnalyses.so
 lib/libosimCommon.so
 lib/libosimExampleComponents.so
-%%JAVA%%lib/libosimJavaJNI.so
+lib/libosimJavaJNI.so
 lib/libosimLepton.so
+lib/libosimMoco.so
 lib/libosimSimulation.so
 lib/libosimTools.so
+lib/libosimdocopt.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/README.md
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/_actuators.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/_analyses.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/_common.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/_examplecomponents.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/_moco.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/_simbody.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/_simulation.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/_tools.so
@@ -376,14 +485,18 @@ lib/libosimTools.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/analyses.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/common.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/examplecomponents.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/moco.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/report.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/simbody.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/simulation.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/arm26.osim
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/calibrated_model_imu.osim
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/dataWithNaNsOfDifferentCases.trc
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/futureOrientationInverseKinematics.trc
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/gait10dof18musc_subject01.osim
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/gait2392_cmc_actuators_empty_model.xml
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/gait2392_setup_forward_empty_model.xml
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/orientation_quats.sto
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/std_subject01_walk1_ik.mot
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/storage.sto
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/subject02_grf_HiFreq.mot
@@ -394,6 +507,8 @@ lib/libosimTools.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/test_basics.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/test_component_interface.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/test_consistent_with_jython.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/test_moco.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/test_opensense.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/test_simbody.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/test_simulation_utilities.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/opensim/tests/test_sockets_inputs_outputs.py
@@ -408,6 +523,7 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/APDMDataReaderSettings.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractChannel.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractDataTable.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractGeometryPath.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractInput.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractOutput.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractPathPoint.java
@@ -415,6 +531,7 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractReporter.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractSocket.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/AbstractTool.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ActivationCoordinateActuator.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ActivationFiberLengthMuscle.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ActiveForceLengthCurve.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Actuation.java
@@ -454,6 +571,9 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Bhargava2004MuscleMetabolicsProbe.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameter.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Bhargava2004MuscleMetabolicsProbe_MetabolicMuscleParameterSet.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Bhargava2004SmoothedMuscleMetabolics.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Bhargava2004SmoothedMuscleMetabolics_MuscleParameters.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Blankevoort1991Ligament.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Body.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/BodyActuator.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/BodyIterator.java
@@ -463,7 +583,9 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/BodyScale.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/BodyScaleSet.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/BodySet.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/BoolLike.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Brick.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/BufferedOrientationsReference.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/BushingForce.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/CMCTool.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/CMC_Joint.java
@@ -494,14 +616,18 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ConsoleReporter.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ConsoleReporterVec3.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Constant.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ConstantCurvatureJoint.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ConstantDistanceConstraint.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Constraint.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ConstraintSet.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ContactCylinder.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ContactEllipsoid.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ContactGeometry.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ContactGeometrySet.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ContactHalfSpace.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ContactMesh.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ContactSphere.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ContactTorus.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Control.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ControlConstant.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ControlLinear.java
@@ -530,6 +656,7 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/DataTableVec3.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/DataTableVec6.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/DataTypeMismatch.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/DeGrooteFregly2016Muscle.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Decorations.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/DecorativeArrow.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/DecorativeBrick.java
@@ -552,12 +679,16 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ElasticFoundationForce.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Ellipsoid.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/EllipsoidJoint.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/EmptyComponentPath.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/EmptyFileName.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/EmptyTable.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Event.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExperimentalSensor.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExponentialContactForce.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExpressionBasedBushingForce.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExpressionBasedCoordinateForce.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExpressionBasedFunction.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExpressionBasedPathForce.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExpressionBasedPointToPointForce.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExternalForce.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ExternalLoads.java
@@ -566,10 +697,14 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FiberCompressiveForceLengthCurve.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FiberForceLengthCurve.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FileAdapter.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FileDeletionThrower.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FileDeletionThrowerException.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FileDoesNotExist.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FileExtensionNotFound.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FileIsEmpty.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FileRemover.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Force.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ForceProducer.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ForceReporter.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ForceSet.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/ForceVelocityCurve.java
@@ -582,6 +717,7 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FreeJoint.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Function.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FunctionBasedBushingForce.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FunctionBasedPath.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/FunctionSet.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/GCVSpline.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/GCVSplineSet.java
@@ -596,7 +732,9 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IKMarkerTask.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IKTask.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IKTaskSet.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IMU.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IMUDataReader.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IMUDataReporter.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IMUInverseKinematicsTool.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IMUPlacer.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IO.java
@@ -611,6 +749,7 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/IndexOutOfRange.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InducedAccelerations.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/Inertia.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InputController.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InputDouble.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InputNotConnected.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InputNotFound.java
@@ -621,6 +760,7 @@ lib/libosimTools.so
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InvalidColumn.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InvalidColumnLabel.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InvalidComponentName.java
+%%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InvalidIndices.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InvalidPropertyValue.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InvalidRow.java
 %%JAVA%%%%DATADIR%%/java/org/opensim/modeling/InvalidTable.java
*** 522 LINES SKIPPED ***