Releases 0.38.0 through 0.38.25 recorded the ENV file migration and deliberately left the file at the old path, so 0.38.26 treating a leftover file as a hand-edit replayed the environment as it stood at that upgrade over every `config:set` and `config:unset` made since, reinstating variables and secrets that had been deliberately unset. A file found at the old path once its migration is on record is no longer imported: it is removed when it agrees with the current config, and is otherwise moved aside to `ENV.migrated` with the keys it disagrees on named in a warning. That warning now reaches the operator during an upgrade rather than being swallowed, which is why the overwrite went unreported.
Install steps run in alphabetical order of the enabled plugin directory, so `apps`, `builder`, and `checks` read an app's environment before the `config` plugin had moved the `ENV` file to its new location. The read came back empty, so their deprecated `DOKKU_*` variables were never migrated to the matching plugin property and were never unset, with nothing reported either way: `dokku config:show` kept listing the variable while the plugin behaved as though it were unset. The relocation now runs before any deprecated variable is read, whatever the install order, and each old file is removed as soon as it has been drained rather than on a later install, which also covers the global file that was never removed at all. A file that reappears at the old path can only have been written by hand, so it is merged in with a warning naming its keys instead of being discarded.
