revert incorrect fix for put updating shadow_index, fixes #5661

A) the compaction code needs the shadow index only for this case:

segment A: PUT x, segment B: DEL x, with A < B  (DEL shadows the PUT).

B) for the following case, we have no shadowing DEL (or rather: it does not matter,
because there is a PUT right after the DEL) and x is in the repo index,
thus the shadow_index is not needed for the special case in the compaction code:

segment A: PUT x, segment B: DEL x PUT x

see also PR #5636.

reverts f079a83fed91c1221951303f758187987be0ac47
and clarifies the code by more comments.

we keep the code deduplication of 5f32b5666af961f5256221660a7356d467f66605
and just add a update_shadow_index param to make it not look like there was
something accidentally forgotten, which was the whole reason for the reverted
"fix".

src/borg/repository.py

@@ -1191,9 +1191,11 @@ class Repository:
         except KeyError:
             pass
         else:
-            # note: doing a delete first will do some bookkeeping,
-            # like updating the shadow_index, quota, ...
-            self._delete(id, segment, offset)
+            # note: doing a delete first will do some bookkeeping.
+            # we do not want to update the shadow_index here, because
+            # we know already that we will PUT to this id, so it will
+            # be in the repo index (and we won't need it in the shadow_index).
+            self._delete(id, segment, offset, update_shadow_index=False)
         segment, offset = self.io.write_put(id, data)
         self.storage_quota_use += len(data) + self.io.put_header_fmt.size
         self.segments.setdefault(segment, 0)
@@ -1216,11 +1218,16 @@ class Repository:
             segment, offset = self.index.pop(id)
         except KeyError:
             raise self.ObjectNotFound(id, self.path) from None
-        self._delete(id, segment, offset)
+        # if we get here, there is an object with this id in the repo,
+        # we write a DEL here that shadows the respective PUT.
+        # after the delete, the object is not in the repo index any more,
+        # for the compaction code, we need to update the shadow_index in this case.
+        self._delete(id, segment, offset, update_shadow_index=True)
 
-    def _delete(self, id, segment, offset):
+    def _delete(self, id, segment, offset, *, update_shadow_index):
         # common code used by put and delete
-        self.shadow_index.setdefault(id, []).append(segment)
+        if update_shadow_index:
+            self.shadow_index.setdefault(id, []).append(segment)
         self.segments[segment] -= 1
         size = self.io.read(segment, offset, id, read_data=False)
         self.storage_quota_use -= size