Fix: tools: crm_shadow --commit now works with CIB_file

Previously, when the CIB_file environment variable was set and
crm_shadow --commit --force was called, the changes from the shadow
file weren't written to the CIB_file. The changes were made only in
memory.

This commit fixes the issue by calling cib_delete(), which writes out
any changes via cib_file_signoff().

Closes T633

Signed-off-by: Reid Wahl <nrwahl@protonmail.com>