`UpdateAllCols` is dangerous, the columns should be updated when
necessary.
This PR replaces some `updateRepository` invokes to reduce possible
problems and wrongly updated time. Some parts have been fixed in #34388,
but some are hidden in the function `updateRepository`. Alternatively,
using `UpdateRepositoryColsNoAutoTime` to update the changed columns.
Some `UpdateRepoSize` invokes are duplicated, so they will be removed
when extracting from `updateRepository`.
224aa64cd9