fix old serialized S4 instances

Global functions
.check_git_repo_is_workable	Source code
.collect_files	Source code
.find_git	Source code
.git_clone_bioc_package	Source code
.git_commit_all_changes	Source code
.git_pull	Source code
.git_push	Source code
.infer_pkgname_from_path	Source code
.is_git_repo	Source code
.is_try_error	Source code
.readLinesWithEOLs	Source code
.run_git_command	Source code
.small_version_bump	Source code
.system3	Source code
.update_dcf_field	Source code
.update_object	Source code
bump_pkg_version	Man page Source code
capture_message	Source code
collect_rda_files	Man page Source code
collect_rds_files	Man page Source code
find_python	Source code
get_descpath	Source code
git-utils	Man page
git_commit	Man page Source code
prepare_git_repo_for_work	Man page Source code
set_git_user_email	Man page Source code
set_git_user_name	Man page Source code
unset_git_user_email	Man page Source code
unset_git_user_name	Man page Source code
updateAllBiocPackageRepoObjects	Man page Source code
updateAllPackageObjects	Man page Source code
updateBiocPackageRepoObjects	Man page Source code
updatePackageObjects	Man page Source code
updateSerializedObjects	Man page Source code
update_rda_file	Man page Source code
update_rds_file	Man page Source code