objects: use object IDs and references instead of naive objs in status/transfer (#6360)

* objects.status: use object IDs instead of naive objects

* objects.transfer: use object IDs instead of naive objects

* objects: add ReferenceHashFile

* odb: add ReferenceObjectDB

* repo: collect used object IDs instead of naive objs

* support basic/naive fs serialization

* objects.stage: stage file objects in addition to trees

* objects: remove save(), update transfer()

* output/dep: update for osave removal

* path_info: support both url and path attributes

* status/gc: use object IDs instead of naive objs

* diff: update staging usage

* commit: update staging usage

* tests: clean staging when needed

* tests: update for save/transfer/stage changes

* dvcfs: don't allow config serialization (repofs should be used instead)

* utils: return mtime as str, size as int

* tests: update unit tests for save/stage/transfer changes

* objects: use Repo.open when needed in ReferenceHashFile

* fix ls test staging

* objects.stage: don't skip hash check when loading from state

- individual hashes will still be loaded from state if they are still
  valid

* ReferenceHashFile: serialize repo fs paths relative to repo root

* preserve state when staging

* objects.tree: skip hash computation in digest() when we have already
loaded hash from state

* always check file existence in referencehashfile

* update repofs test since stage no longer allows nonexistent files

* odb: only protect on check() if hash was verified

* staging: use unique memfs namespace for staging per dest ODB

* tests: clean full staging namespace

* refodb: preserve repofs cache dir

* repodependency: stage imports to local ODB and strict check circular
imports

* fetch: fetch staging last

* staging: make dest odb mandatory and preserve state

* refodb: cache nonlocal fs's

* fix rebase errors

* repofs: support full instantiation from fs config

* repofs: preserve subrepo factory for erepos

* tests: clarify repofs dirty file behavior

tests/func/objects/db/test_index.py

@@ -4,6 +4,7 @@ from dvc.exceptions import DownloadError, UploadError
 from dvc.fs.local import LocalFileSystem
 from dvc.objects.db import get_index
 from dvc.utils.fs import remove
+from tests.utils import clean_staging
 
 
 @pytest.fixture
@@ -16,6 +17,7 @@ def test_indexed_on_status(tmp_dir, dvc, index):
     foo = tmp_dir.dvc_gen({"foo": "foo content"})[0].outs[0]
     bar = tmp_dir.dvc_gen({"bar": {"baz": "baz content"}})[0].outs[0]
     baz_hash = bar.obj.trie.get(("baz",)).hash_info
+    clean_staging()
     dvc.push()
     index.clear()
 
@@ -29,6 +31,7 @@ def test_indexed_on_push(tmp_dir, dvc, index):
     foo = tmp_dir.dvc_gen({"foo": "foo content"})[0].outs[0]
     bar = tmp_dir.dvc_gen({"bar": {"baz": "baz content"}})[0].outs[0]
     baz_hash = bar.obj.trie.get(("baz",)).hash_info
+    clean_staging()
 
     dvc.push()
     assert {bar.hash_info.value, baz_hash.value} == set(index.hashes())