"Assume unchanged" git: do not set CE_VALID with --refresh

When working with automatic assume-unchanged mode using
core.ignorestat, setting CE_VALID after --refresh makes things
more cumbersome to use.  Consider this scenario:

 (1) the working tree is on a filesystem with slow lstat(2).
     The user sets core.ignorestat = true.

 (2) "git checkout" to switch to a different branch (or initial
     checkout) updates all paths and the index starts out with
     "all clean".

 (3) The user knows she wants to edit certain paths.  She uses
     update-index --no-assume-unchanged (we could call it --edit;
     the name is inmaterial) to mark these paths and starts
     editing.

 (4) After editing half of the paths marked to be edited, she
     runs "git status".  This runs "update-index --refresh" to
     reduce the false hits from diff-files.

 (5) Now the other half of the paths, since she has not changed
     them, are found to match the index, and CE_VALID is set on
     them again.

For this reason, this commit makes update-index --refresh not to
set CE_VALID even after the path without CE_VALID are verified
to be up to date.  The user still can run --really-refresh to
force lstat() to match the index entries to the reality.

Signed-off-by: Junio C Hamano <junkio@cox.net>

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