docker: fix stale directory tree with volume mount

Some rsync options are actually conflicting options (even though rsync
doesn't say so), which may lead to a stale tree in the case of Docker
volume mounts if the Docker image is generated after the modifications
in the mounted tree.

tools/docker/scripts/ci_entrypoint.sh

@@ -25,13 +25,17 @@ if [ -n "${GIT_REF}" ]; then
 
 elif [ -d  /mnt/cp2k ]; then
     echo -e "\n========== Copying Changed Files =========="
-    rsync --update                               \
+    # Don't skip by matching timestamp since Git (previous mirror) does not preserve timestamps
+    # and we end up with an outdated tree if the contents of /mnt/cp2k have been modified before
+    # the Docker image was generated.
+    # Also ignore the checksum since it is safe to assume that most files have not changed (which would
+    # mean they have the same filesize) which would mean we would do a read+read(+write) on most files
+    # anyway at which point it is simpler to do a read+write (e.g. replace the whole tree).
+    rsync --ignore-times                         \
           --delete                               \
           --executability                        \
-          --ignore-times                         \
           --verbose                              \
           --recursive                            \
-          --checksum                             \
           --exclude="*~"                         \
           --exclude=".*/"                        \
           --exclude="*.py[cod]"                  \