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.