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dirstatemap: add a common `_refresh_entry` method for dirstatemap

Authored by marmoute.

Description

dirstatemap: add a common _refresh_entry method for dirstatemap

This method is called once a DirstateItem have been modified to apply the
change on the dirstatemap if necessary.

Each variant have a different implementation (which is … the point).

We use addfile for the rustmap and not set_dirstate_item because we need to
keep the internal counter up to date and set_dirstate_item does not do it.

Differential Revision: https://phab.mercurial-scm.org/D11571