fix the repair mode

if one used --last (or since shortly: gave an archive name), verify_chunks (old method name) was
not called because it requires all archives having been checked.

the problem was that also the final manifest.write() and repository.commit() was done in that method,
so all other repair work did not get committed in that case.

I moved these calls that to a separate finish() method.

borg/archive.py

@@ -611,6 +611,7 @@ def __init__(self):
 
     def check(self, repository, repair=False, archive=None, last=None):
         self.report_progress('Starting archive consistency check...')
+        self.check_all = archive is None and last is None
         self.repair = repair
         self.repository = repository
         self.init_chunks()
@@ -620,10 +621,8 @@ def check(self, repository, repair=False, archive=None, last=None):
         else:
             self.manifest, _ = Manifest.load(repository, key=self.key)
         self.rebuild_refcounts(archive=archive, last=last)
-        if last is None and archive is None:
-            self.verify_chunks()
-        else:
-            self.report_progress('Orphaned objects check skipped (needs all archives checked)')
+        self.orphan_chunks_check()
+        self.finish()
         if not self.error_found:
             self.report_progress('Archive consistency check complete, no problems found.')
         return self.repair or not self.error_found
@@ -803,16 +802,22 @@ def missing_chunk_detector(chunk_id):
             add_reference(new_archive_id, len(data), len(cdata), cdata)
             info[b'id'] = new_archive_id
 
-    def verify_chunks(self):
-        unused = set()
-        for id_, (count, size, csize) in self.chunks.iteritems():
-            if count == 0:
-                unused.add(id_)
-        orphaned = unused - self.possibly_superseded
-        if orphaned:
-            self.report_progress('{} orphaned objects found'.format(len(orphaned)), error=True)
+    def orphan_chunks_check(self):
+        if self.check_all:
+            unused = set()
+            for id_, (count, size, csize) in self.chunks.iteritems():
+                if count == 0:
+                    unused.add(id_)
+            orphaned = unused - self.possibly_superseded
+            if orphaned:
+                self.report_progress('{} orphaned objects found'.format(len(orphaned)), error=True)
+            if self.repair:
+                for id_ in unused:
+                    self.repository.delete(id_)
+        else:
+            self.report_progress('Orphaned objects check skipped (needs all archives checked)')
+
+    def finish(self):
         if self.repair:
-            for id_ in unused:
-                self.repository.delete(id_)
             self.manifest.write()
             self.repository.commit()