Fix testcases:

1. main.merge fails with errno 13 in copy_file().

The reason for the error is that copy_file tries to create a file with the same name as recently deleted one,
and there is still an open handle for the deleted file.
To fix, use my_delete_allow_opened() for MTR's delete_file. On Windows,  this renames file to unique name
prior to deletion, and prevents EACCES errors for files opened with FILE_SHARE_DELETE.

2. innodb_bug59641 
generates warnings, after server was killed and restarted in the test case.
The warnings are about test_suppression table (needs to be repaired, as it that was written just prior to the crash)
Fixed by using FLUSH TABLES after populating warning suppression table.

client/mysqltest.cc

@@ -3060,7 +3060,7 @@ void do_remove_file(struct st_command *command)
                      ' ');
 
   DBUG_PRINT("info", ("removing file: %s", ds_filename.str));
-  error= my_delete(ds_filename.str, MYF(disable_warnings ? 0 : MY_WME)) != 0;
+  error= my_delete_allow_opened(ds_filename.str, MYF(disable_warnings ? 0 : MY_WME)) != 0;
   handle_command_error(command, error, my_errno);
   dynstr_free(&ds_filename);
   DBUG_VOID_RETURN;

mysql-test/suite/innodb/r/innodb_bug59641.result

@@ -16,6 +16,7 @@ UPDATE t SET b=4*a WHERE a=32;
 XA END '789';
 XA PREPARE '789';
 call mtr.add_suppression("Found 3 prepared XA transactions");
+FLUSH TABLES;
 SET TRANSACTION ISOLATION LEVEL READ UNCOMMITTED;
 SELECT * FROM t;
 a	b

mysql-test/suite/innodb/t/innodb_bug59641.test

@@ -33,7 +33,7 @@ XA PREPARE '789';
 
 # The server would issue this warning on restart.
 call mtr.add_suppression("Found 3 prepared XA transactions");
-
+FLUSH TABLES;
 # Kill the server without sending a shutdown command
 -- exec echo "wait" > $MYSQLTEST_VARDIR/tmp/mysqld.1.expect
 -- shutdown_server 0

mysql-test/suite/innodb_plugin/r/innodb_bug59641.result

@@ -16,6 +16,7 @@ UPDATE t SET b=4*a WHERE a=32;
 XA END '789';
 XA PREPARE '789';
 call mtr.add_suppression("Found 3 prepared XA transactions");
+FLUSH TABLES;
 SET TRANSACTION ISOLATION LEVEL READ UNCOMMITTED;
 SELECT * FROM t;
 a	b

mysql-test/suite/innodb_plugin/t/innodb_bug59641.test

@@ -33,7 +33,7 @@ XA PREPARE '789';
 
 # The server would issue this warning on restart.
 call mtr.add_suppression("Found 3 prepared XA transactions");
-
+FLUSH TABLES;
 # Kill the server without sending a shutdown command
 -- exec echo "wait" > $MYSQLTEST_VARDIR/tmp/mysqld.1.expect
 -- shutdown_server 0