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/test_import.py

@@ -13,6 +13,7 @@ from dvc.stage.exceptions import StagePathNotFoundError
 from dvc.system import System
 from dvc.utils.fs import makedirs, remove
 from tests.unit.fs.test_repo import make_subrepo
+from tests.utils import clean_staging
 
 
 def test_import(tmp_dir, scm, dvc, erepo_dir):
@@ -290,6 +291,8 @@ def test_push_wildcard_from_bare_git_repo(
     dvc_repo = make_tmp_dir("dvc-repo", scm=True, dvc=True)
     with dvc_repo.chdir():
         dvc_repo.dvc.imp(os.fspath(tmp_dir), "dirextra")
+        clean_staging()
+
         with pytest.raises(PathMissingError):
             dvc_repo.dvc.imp(os.fspath(tmp_dir), "dir123")
 
@@ -593,6 +596,7 @@ def test_circular_import(tmp_dir, dvc, scm, erepo_dir):
     dvc.imp(os.fspath(erepo_dir), "dir", "dir_imported")
     scm.add("dir_imported.dvc")
     scm.commit("import")
+    clean_staging()
 
     with erepo_dir.chdir():
         with pytest.raises(CircularImportError):