Not sure if this is going to be a part of the forthcoming Migrator product but thought I should mention this:
I use Snapshot Pro to do full cloud based backups of sites. At least one of these sites has multiple security plugins (ie wordfence), ithemes security etc. and is on a cpanel based server (compared to my dev server which is debian and not a hint of cpanel).
When I used the snapshot installer (or tried to) to restore/migrate the backup to create an updated dev site it encountered a problem.
Other than the obvious (someone in the past has editted this particular site so the WP_CONTENT_DIR setting is moved) we also had a rather unique problem in that the settings in .htaccess/.user.ini not only stopped the site working, they also killed the snapshot installer from working (path issues/wordfence firewall path and various others).
It would be nice to have an option to have these critical files restored as a backup file (ie restore.htaccess) and have a default .htaccess/.user.ini file restored in their place OR ensure that these specific files only get restored once everything else is restored so the restore happens before its, potentially, killed as these files can have entries that will kill the web process trying to do the restore.