refine 1->3 upgrade process

In hindsight, the "post_tx" step in the upgrade process introduced in
e7f5733 doesn't make sense. If the procedure fails at this stage, nothing says
it still needs to be completed. If the sample file dirs have to be updated
after the database, then there should be another database version to mark that
it's fully completed, and indeed that's the purpose version 3 serves. So get
rid of the Upgrader trait and just go back to a simple run function per
version.

In the case of the sample file dir metadata, it actually can happen before the
database transaction; the stuff written to the database later just needs to be
consistent with what it finds if there's an existing metadata file from a
half-completed update.

For safety, ensure there are no unexpected directory contents before
upgrading 1->2, and ensure the metadata matches before upgrading 2->3.

src/cmds/mod.rs

@@ -75,7 +75,7 @@ enum OpenMode {
 /// Locks and opens the database.
 /// The returned `dir::Fd` holds the lock and should be kept open as long as the `Connection` is.
 fn open_conn(db_dir: &str, mode: OpenMode) -> Result<(dir::Fd, rusqlite::Connection), Error> {
-    let dir = dir::Fd::open(None, db_dir, mode == OpenMode::Create)?;
+    let dir = dir::Fd::open(db_dir, mode == OpenMode::Create)?;
     let ro = mode == OpenMode::ReadOnly;
     dir.lock(if ro { libc::LOCK_SH } else { libc::LOCK_EX } | libc::LOCK_NB)
        .map_err(|e| e.context(format!("db dir {:?} already in use; can't get {} lock",