Fix OMSimulator submodule update when directory layout changes

Clean the working tree (including nested git repos) before running
submodule update, so that directories that were replaced by submodules
(or vice versa) don't block initialization.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: AnHeuermann

.CI/Jenkinsfile

@@ -715,8 +715,9 @@ def runRegressiontest(branch, name, extraFlags, omsHash, dbPrefix, sshConfig, om
 
     if ! (cmp ~/saved_omc/OMSimulator/.githash .newhash); then
 
-      git submodule update || exit 1
-      git clean -fdx || exit 1
+      git submodule sync --recursive || exit 1
+      git clean -ffdx || exit 1
+      git submodule update --init --recursive --force || exit 1
       git submodule foreach --recursive  "git fetch --tags --force && git reset --hard && git clean -fdxq -e /git -e /svn" || exit 1
       cmake -S . -B build/ -DCMAKE_INSTALL_PREFIX=install/
       cmake --build build/ --target install || exit 1