That issue was not on my own computer. Git version is something like 2.10.
We started to monitor file system with Process Monitor (https://technet.microsoft.com/ru-ru/sysinternals/processmonitor.aspx).

On "bad" computer there only records like at screenshot. All files in repository was opened.

I compared the output of git ls-files --debug between two computers and saw that there were differences in mtime flag. I tried to understand what mtime means. mtime is the "modified time", right?
I opened libgit2 source code and found that if comment mtime check, that fixes slow performance on "bad" computer:

----------------------- src/diff_generate.c -----------------------------
index e11cbe4e4..b3e9a37c0 100644
@@ -817,8 +817,9 @@ static int maybe_modified(
 			modified_uncertain =
 				(oitem->file_size <= 0 && nitem->file_size > 0);
 		}
-		else if (!git_index_time_eq(&oitem->mtime, &nitem->mtime) ||
-			(use_ctime && !git_index_time_eq(&oitem->ctime, &nitem->ctime)) ||
+		else if (
+			/*!git_index_time_eq(&oitem->mtime, &nitem->mtime) ||
+			(use_ctime && !git_index_time_eq(&oitem->ctime, &nitem->ctime)) ||*/
 			oitem->ino != nitem->ino ||
 			oitem->uid != nitem->uid ||
 			oitem->gid != nitem->gid ||
@@ -859,7 +860,7 @@ static int maybe_modified(
 	 * and an add of the new so that consumers can act accordingly (eg,
 	 * checkout will update the case on disk.)
 	 */
-	if (DIFF_FLAG_IS_SET(diff, GIT_DIFF_IGNORE_CASE) &&
+	/*if (DIFF_FLAG_IS_SET(diff, GIT_DIFF_IGNORE_CASE) &&
 		DIFF_FLAG_IS_SET(diff, GIT_DIFF_INCLUDE_CASECHANGE) &&
 		strcmp(oitem->path, nitem->path) != 0) {
 
@@ -867,7 +868,7 @@ static int maybe_modified(
 			error = diff_delta__from_one(diff, GIT_DELTA_ADDED, NULL, nitem);
 
 		return error;
-	}
+	}*/
 
 	return diff_delta__from_two(
 		diff, status, oitem, omode, nitem, nmode,

RetrieveStatus take so long time about 5s #1570

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