diff --git a/.changes/unreleased/Under the Hood-20231108-163613.yaml b/.changes/unreleased/Under the Hood-20231108-163613.yaml
new file mode 100644
index 00000000000..091c09bfe32
--- /dev/null
+++ b/.changes/unreleased/Under the Hood-20231108-163613.yaml	
@@ -0,0 +1,6 @@
+kind: Under the Hood
+body: Consolidate deferral methods & flags
+time: 2023-11-08T16:36:13.234324-05:00
+custom:
+  Author: jtcohen6
+  Issue: 7965 8715
diff --git a/core/dbt/cli/flags.py b/core/dbt/cli/flags.py
index ffc73323df8..706370609ca 100644
--- a/core/dbt/cli/flags.py
+++ b/core/dbt/cli/flags.py
@@ -113,6 +113,7 @@ def _get_params_by_source(ctx: Context, source_type: ParameterSource):
         def _assign_params(
             ctx: Context,
             params_assigned_from_default: set,
+            params_assigned_from_user: set,
             deprecated_env_vars: Dict[str, Callable],
         ):
             """Recursively adds all click params to flag object"""
@@ -178,15 +179,30 @@ def _assign_params(
                     object.__setattr__(self, flag_name, param_value)
 
                 # Track default assigned params.
-                if is_default:
+                # For flags that are accepted at both 'parent' and 'child' levels,
+                # we need to track user-provided and default values across both,
+                # to support detection of mutually exclusive flags later on.
+                if not is_default:
+                    params_assigned_from_user.add(param_name)
+                    if param_name in params_assigned_from_default:
+                        params_assigned_from_default.remove(param_name)
+                if is_default and param_name not in params_assigned_from_user:
                     params_assigned_from_default.add(param_name)
 
             if ctx.parent:
-                _assign_params(ctx.parent, params_assigned_from_default, deprecated_env_vars)
+                _assign_params(
+                    ctx.parent,
+                    params_assigned_from_default,
+                    params_assigned_from_user,
+                    deprecated_env_vars,
+                )
 
+        params_assigned_from_user = set()  # type: Set[str]
         params_assigned_from_default = set()  # type: Set[str]
         deprecated_env_vars: Dict[str, Callable] = {}
-        _assign_params(ctx, params_assigned_from_default, deprecated_env_vars)
+        _assign_params(
+            ctx, params_assigned_from_default, params_assigned_from_user, deprecated_env_vars
+        )
 
         # Set deprecated_env_var_warnings to be fired later after events have been init.
         object.__setattr__(
@@ -203,7 +219,10 @@ def _assign_params(
             invoked_subcommand.ignore_unknown_options = True
             invoked_subcommand_ctx = invoked_subcommand.make_context(None, sys.argv)
             _assign_params(
-                invoked_subcommand_ctx, params_assigned_from_default, deprecated_env_vars
+                invoked_subcommand_ctx,
+                params_assigned_from_default,
+                params_assigned_from_user,
+                deprecated_env_vars,
             )
 
         if not project_flags:
@@ -378,7 +397,11 @@ def add_fn(x):
         if k == "macro" and command == CliCommand.RUN_OPERATION:
             add_fn(v)
         # None is a Singleton, False is a Flyweight, only one instance of each.
-        elif v is None or v is False:
+        elif (v is None or v is False) and k not in (
+            # These are None by default but they do not support --no-{flag}
+            "defer_state",
+            "log_format",
+        ):
             add_fn(f"--no-{spinal_cased}")
         elif v is True:
             add_fn(f"--{spinal_cased}")
diff --git a/core/dbt/cli/main.py b/core/dbt/cli/main.py
index 3525de95f96..51bb3d6d9bd 100644
--- a/core/dbt/cli/main.py
+++ b/core/dbt/cli/main.py
@@ -121,11 +121,19 @@ def invoke(self, args: List[str], **kwargs) -> dbtRunnerResult:
 def global_flags(func):
     @p.cache_selected_only
     @p.debug
+    @p.defer
+    @p.deprecated_defer
+    @p.defer_state
+    @p.deprecated_favor_state
     @p.deprecated_print
+    @p.deprecated_state
     @p.enable_legacy_logger
     @p.fail_fast
+    @p.favor_state
+    @p.indirect_selection
     @p.log_cache_events
     @p.log_file_max_bytes
+    @p.log_format
     @p.log_format_file
     @p.log_level
     @p.log_level_file
@@ -141,12 +149,15 @@ def global_flags(func):
     @p.record_timing_info
     @p.send_anonymous_usage_stats
     @p.single_threaded
+    @p.state
     @p.static_parser
     @p.use_colors
     @p.use_colors_file
     @p.use_experimental_parser
     @p.version
     @p.version_check
+    @p.warn_error
+    @p.warn_error_options
     @p.write_json
     @functools.wraps(func)
     def wrapper(*args, **kwargs):
@@ -164,9 +175,6 @@ def wrapper(*args, **kwargs):
 )
 @click.pass_context
 @global_flags
-@p.warn_error
-@p.warn_error_options
-@p.log_format
 @p.show_resource_report
 def cli(ctx, **kwargs):
     """An ELT tool for managing your SQL transformations and data models.
@@ -178,14 +186,9 @@ def cli(ctx, **kwargs):
 @cli.command("build")
 @click.pass_context
 @global_flags
-@p.defer
-@p.deprecated_defer
 @p.exclude
-@p.favor_state
-@p.deprecated_favor_state
 @p.full_refresh
 @p.include_saved_query
-@p.indirect_selection
 @p.profile
 @p.profiles_dir
 @p.project_dir
@@ -193,9 +196,6 @@ def cli(ctx, **kwargs):
 @p.select
 @p.selector
 @p.show
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.store_failures
 @p.target
 @p.target_path
@@ -257,11 +257,7 @@ def docs(ctx, **kwargs):
 @click.pass_context
 @global_flags
 @p.compile_docs
-@p.defer
-@p.deprecated_defer
 @p.exclude
-@p.favor_state
-@p.deprecated_favor_state
 @p.profile
 @p.profiles_dir
 @p.project_dir
@@ -269,9 +265,6 @@ def docs(ctx, **kwargs):
 @p.selector
 @p.empty_catalog
 @p.static
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.target
 @p.target_path
 @p.threads
@@ -328,14 +321,9 @@ def docs_serve(ctx, **kwargs):
 @cli.command("compile")
 @click.pass_context
 @global_flags
-@p.defer
-@p.deprecated_defer
 @p.exclude
-@p.favor_state
-@p.deprecated_favor_state
 @p.full_refresh
 @p.show_output_format
-@p.indirect_selection
 @p.introspect
 @p.profile
 @p.profiles_dir
@@ -344,9 +332,6 @@ def docs_serve(ctx, **kwargs):
 @p.select
 @p.selector
 @p.inline
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.compile_inject_ephemeral_ctes
 @p.target
 @p.target_path
@@ -376,15 +361,10 @@ def compile(ctx, **kwargs):
 @cli.command("show")
 @click.pass_context
 @global_flags
-@p.defer
-@p.deprecated_defer
 @p.exclude
-@p.favor_state
-@p.deprecated_favor_state
 @p.full_refresh
 @p.show_output_format
 @p.show_limit
-@p.indirect_selection
 @p.introspect
 @p.profile
 @p.profiles_dir
@@ -392,9 +372,6 @@ def compile(ctx, **kwargs):
 @p.select
 @p.selector
 @p.inline
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.target
 @p.target_path
 @p.threads
@@ -514,7 +491,6 @@ def init(ctx, **kwargs):
 @click.pass_context
 @global_flags
 @p.exclude
-@p.indirect_selection
 @p.models
 @p.output
 @p.output_keys
@@ -524,9 +500,6 @@ def init(ctx, **kwargs):
 @p.resource_type
 @p.raw_select
 @p.selector
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.target
 @p.target_path
 @p.vars
@@ -582,10 +555,6 @@ def parse(ctx, **kwargs):
 @cli.command("run")
 @click.pass_context
 @global_flags
-@p.defer
-@p.deprecated_defer
-@p.favor_state
-@p.deprecated_favor_state
 @p.exclude
 @p.full_refresh
 @p.profile
@@ -594,9 +563,6 @@ def parse(ctx, **kwargs):
 @p.empty
 @p.select
 @p.selector
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.target
 @p.target_path
 @p.threads
@@ -629,7 +595,6 @@ def run(ctx, **kwargs):
 @p.vars
 @p.profile
 @p.target
-@p.state
 @p.threads
 @p.full_refresh
 @requires.postflight
@@ -654,7 +619,6 @@ def retry(ctx, **kwargs):
 @cli.command("clone")
 @click.pass_context
 @global_flags
-@p.defer_state
 @p.exclude
 @p.full_refresh
 @p.profile
@@ -663,7 +627,6 @@ def retry(ctx, **kwargs):
 @p.resource_type
 @p.select
 @p.selector
-@p.state  # required
 @p.target
 @p.target_path
 @p.threads
@@ -731,9 +694,6 @@ def run_operation(ctx, **kwargs):
 @p.select
 @p.selector
 @p.show
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.target
 @p.target_path
 @p.threads
@@ -760,19 +720,12 @@ def seed(ctx, **kwargs):
 @cli.command("snapshot")
 @click.pass_context
 @global_flags
-@p.defer
-@p.deprecated_defer
 @p.exclude
-@p.favor_state
-@p.deprecated_favor_state
 @p.profile
 @p.profiles_dir
 @p.project_dir
 @p.select
 @p.selector
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.target
 @p.target_path
 @p.threads
@@ -815,9 +768,6 @@ def source(ctx, **kwargs):
 @p.project_dir
 @p.select
 @p.selector
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.target
 @p.target_path
 @p.threads
@@ -851,20 +801,12 @@ def freshness(ctx, **kwargs):
 @cli.command("test")
 @click.pass_context
 @global_flags
-@p.defer
-@p.deprecated_defer
 @p.exclude
-@p.favor_state
-@p.deprecated_favor_state
-@p.indirect_selection
 @p.profile
 @p.profiles_dir
 @p.project_dir
 @p.select
 @p.selector
-@p.state
-@p.defer_state
-@p.deprecated_state
 @p.store_failures
 @p.target
 @p.target_path
diff --git a/core/dbt/context/providers.py b/core/dbt/context/providers.py
index 1f99665af7e..3064a1baa81 100644
--- a/core/dbt/context/providers.py
+++ b/core/dbt/context/providers.py
@@ -1406,7 +1406,8 @@ def sql(self) -> Optional[str]:
         if self.model.language == ModelLanguage.sql:  # type: ignore[union-attr]
             # If the model is deferred and the adapter doesn't support zero-copy cloning, then select * from the prod
             # relation
-            if getattr(self.model, "defer_relation", None):
+            # TODO: avoid routing on args.which if possible
+            if getattr(self.model, "defer_relation", None) and self.config.args.which == "clone":
                 # TODO https://github.com/dbt-labs/dbt-core/issues/7976
                 return f"select * from {self.model.defer_relation.relation_name or str(self.defer_relation)}"  # type: ignore[union-attr]
             elif getattr(self.model, "extra_ctes_injected", None):
diff --git a/core/dbt/contracts/graph/manifest.py b/core/dbt/contracts/graph/manifest.py
index 426b99d39b6..f0e090c95d9 100644
--- a/core/dbt/contracts/graph/manifest.py
+++ b/core/dbt/contracts/graph/manifest.py
@@ -1341,7 +1341,7 @@ def is_invalid_protected_ref(
             node.package_name != target_model.package_name and restrict_package_access
         )
 
-    # Called by RunTask.defer_to_manifest
+    # Called by GraphRunnableTask.defer_to_manifest
     def merge_from_artifact(
         self,
         adapter,
@@ -1370,6 +1370,13 @@ def merge_from_artifact(
                 merged.add(unique_id)
                 self.nodes[unique_id] = node.replace(deferred=True)
 
+            # for all other nodes, add 'defer_relation'
+            elif current and node.resource_type in refables and not node.is_ephemeral:
+                defer_relation = DeferRelation(
+                    node.database, node.schema, node.alias, node.relation_name
+                )
+                self.nodes[unique_id] = current.replace(defer_relation=defer_relation)
+
         # Rebuild the flat_graph, which powers the 'graph' context variable,
         # now that we've deferred some nodes
         self.build_flat_graph()
@@ -1378,25 +1385,6 @@ def merge_from_artifact(
         sample = list(islice(merged, 5))
         fire_event(MergedFromState(num_merged=len(merged), sample=sample))
 
-    # Called by CloneTask.defer_to_manifest
-    def add_from_artifact(
-        self,
-        other: "WritableManifest",
-    ) -> None:
-        """Update this manifest by *adding* information about each node's location
-        in the other manifest.
-
-        Only non-ephemeral refable nodes are examined.
-        """
-        refables = set(NodeType.refable())
-        for unique_id, node in other.nodes.items():
-            current = self.nodes.get(unique_id)
-            if current and (node.resource_type in refables and not node.is_ephemeral):
-                defer_relation = DeferRelation(
-                    node.database, node.schema, node.alias, node.relation_name
-                )
-                self.nodes[unique_id] = current.replace(defer_relation=defer_relation)
-
     # Methods that were formerly in ParseResult
 
     def add_macro(self, source_file: SourceFile, macro: Macro):
diff --git a/core/dbt/task/clone.py b/core/dbt/task/clone.py
index 849eec1c8b1..ef595afef7f 100644
--- a/core/dbt/task/clone.py
+++ b/core/dbt/task/clone.py
@@ -1,15 +1,15 @@
 import threading
-from typing import AbstractSet, Any, List, Iterable, Set
+from typing import AbstractSet, Any, List, Iterable, Set, Optional
 
 from dbt.adapters.base import BaseRelation
 from dbt.clients.jinja import MacroGenerator
 from dbt.context.providers import generate_runtime_model_context
+from dbt.contracts.graph.manifest import WritableManifest
 from dbt.artifacts.run import RunStatus, RunResult
 from dbt.common.dataclass_schema import dbtClassMixin
 from dbt.common.exceptions import DbtInternalError, CompilationError
 from dbt.graph import ResourceTypeSelector
 from dbt.node_types import NodeType
-from dbt.parser.manifest import write_manifest
 from dbt.task.base import BaseRunner
 from dbt.task.run import _validate_materialization_relations_dict
 from dbt.task.runnable import GraphRunnableTask
@@ -94,6 +94,11 @@ class CloneTask(GraphRunnableTask):
     def raise_on_first_error(self):
         return False
 
+    def _get_deferred_manifest(self) -> Optional[WritableManifest]:
+        # Unlike other commands, 'clone' always requires a state manifest
+        # Load previous state, regardless of whether --defer flag has been set
+        return self._get_previous_state()
+
     def get_model_schemas(self, adapter, selected_uids: Iterable[str]) -> Set[BaseRelation]:
         if self.manifest is None:
             raise DbtInternalError("manifest was None in get_model_schemas")
@@ -154,17 +159,3 @@ def get_node_selector(self) -> ResourceTypeSelector:
 
     def get_runner_type(self, _):
         return CloneRunner
-
-    # Note that this is different behavior from --defer with other commands, which *merge*
-    # selected nodes from this manifest + unselected nodes from the other manifest
-    def defer_to_manifest(self, adapter, selected_uids: AbstractSet[str]):
-        deferred_manifest = self._get_deferred_manifest()
-        if deferred_manifest is None:
-            return
-        if self.manifest is None:
-            raise DbtInternalError(
-                "Expected to defer to manifest, but there is no runtime manifest to defer from!"
-            )
-        self.manifest.add_from_artifact(other=deferred_manifest)
-        # TODO: is it wrong to write the manifest here? I think it's right...
-        write_manifest(self.manifest, self.config.target_path)
diff --git a/core/dbt/task/compile.py b/core/dbt/task/compile.py
index 4d6e049b359..1c20a41e07e 100644
--- a/core/dbt/task/compile.py
+++ b/core/dbt/task/compile.py
@@ -1,7 +1,5 @@
 import threading
-from typing import AbstractSet, Optional
 
-from dbt.contracts.graph.manifest import WritableManifest
 from dbt.artifacts.run import RunStatus, RunResult
 from dbt.common.events.base_types import EventLevel
 from dbt.common.events.functions import fire_event
@@ -15,7 +13,7 @@
 
 from dbt.graph import ResourceTypeSelector
 from dbt.node_types import NodeType
-from dbt.parser.manifest import write_manifest, process_node
+from dbt.parser.manifest import process_node
 from dbt.parser.sql import SqlBlockParser
 from dbt.task.base import BaseRunner
 from dbt.task.runnable import GraphRunnableTask
@@ -101,26 +99,6 @@ def task_end_messages(self, results):
                 )
             )
 
-    def _get_deferred_manifest(self) -> Optional[WritableManifest]:
-        return super()._get_deferred_manifest() if self.args.defer else None
-
-    def defer_to_manifest(self, adapter, selected_uids: AbstractSet[str]):
-        deferred_manifest = self._get_deferred_manifest()
-        if deferred_manifest is None:
-            return
-        if self.manifest is None:
-            raise DbtInternalError(
-                "Expected to defer to manifest, but there is no runtime manifest to defer from!"
-            )
-        self.manifest.merge_from_artifact(
-            adapter=adapter,
-            other=deferred_manifest,
-            selected=selected_uids,
-            favor_state=bool(self.args.favor_state),
-        )
-        # TODO: is it wrong to write the manifest here? I think it's right...
-        write_manifest(self.manifest, self.config.project_target_path)
-
     def _runtime_initialize(self):
         if getattr(self.args, "inline", None):
             try:
diff --git a/core/dbt/task/freshness.py b/core/dbt/task/freshness.py
index 8301893add9..db4d9ca1075 100644
--- a/core/dbt/task/freshness.py
+++ b/core/dbt/task/freshness.py
@@ -171,10 +171,6 @@ def node_is_match(self, node):
 
 
 class FreshnessTask(GraphRunnableTask):
-    def defer_to_manifest(self, adapter, selected_uids):
-        # freshness don't defer
-        return
-
     def result_path(self):
         if self.args.output:
             return os.path.realpath(self.args.output)
diff --git a/core/dbt/task/list.py b/core/dbt/task/list.py
index 5c5edf421a5..5b2270d141c 100644
--- a/core/dbt/task/list.py
+++ b/core/dbt/task/list.py
@@ -183,10 +183,6 @@ def selection_arg(self):
         else:
             return self.args.select
 
-    def defer_to_manifest(self, adapter, selected_uids):
-        # list don't defer
-        return
-
     def get_node_selector(self):
         if self.manifest is None or self.graph is None:
             raise DbtInternalError("manifest and graph must be set to get perform node selection")
diff --git a/core/dbt/task/runnable.py b/core/dbt/task/runnable.py
index 81f1b4922bd..ddeaf116cde 100644
--- a/core/dbt/task/runnable.py
+++ b/core/dbt/task/runnable.py
@@ -125,9 +125,24 @@ def get_selection_spec(self) -> SelectionSpec:
     def get_node_selector(self) -> NodeSelector:
         raise NotImplementedError(f"get_node_selector not implemented for task {type(self)}")
 
-    @abstractmethod
     def defer_to_manifest(self, adapter, selected_uids: AbstractSet[str]):
-        raise NotImplementedError(f"defer_to_manifest not implemented for task {type(self)}")
+        deferred_manifest = self._get_deferred_manifest()
+        if deferred_manifest is None:
+            return
+        if self.manifest is None:
+            raise DbtInternalError(
+                "Expected to defer to manifest, but there is no runtime manifest to defer from!"
+            )
+        self.manifest.merge_from_artifact(
+            adapter=adapter,
+            other=deferred_manifest,
+            selected=selected_uids,
+            favor_state=bool(self.args.favor_state),
+        )
+        # We're rewriting the manifest because it's been mutated during merge_from_artifact.
+        # This is to reflect which nodes had been deferred to (= replaced with) their counterparts.
+        if self.args.write_json:
+            write_manifest(self.manifest, self.config.project_target_path)
 
     def get_graph_queue(self) -> GraphQueue:
         selector = self.get_node_selector()
@@ -609,7 +624,7 @@ def get_result(self, results, elapsed_time, generated_at):
     def task_end_messages(self, results):
         print_run_end_messages(results)
 
-    def _get_deferred_manifest(self) -> Optional[WritableManifest]:
+    def _get_previous_state(self) -> Optional[WritableManifest]:
         state = self.previous_defer_state or self.previous_state
         if not state:
             raise DbtRuntimeError(
@@ -619,3 +634,6 @@ def _get_deferred_manifest(self) -> Optional[WritableManifest]:
         if not state.manifest:
             raise DbtRuntimeError(f'Could not find manifest in --state path: "{state}"')
         return state.manifest
+
+    def _get_deferred_manifest(self) -> Optional[WritableManifest]:
+        return self._get_previous_state() if self.args.defer else None
diff --git a/core/dbt/task/seed.py b/core/dbt/task/seed.py
index 31dbd241e56..8c9d5279385 100644
--- a/core/dbt/task/seed.py
+++ b/core/dbt/task/seed.py
@@ -62,10 +62,6 @@ def print_result_line(self, result):
 
 
 class SeedTask(RunTask):
-    def defer_to_manifest(self, adapter, selected_uids):
-        # seeds don't defer
-        return
-
     def raise_on_first_error(self):
         return False
 
diff --git a/tests/functional/dbt_runner/test_dbt_runner.py b/tests/functional/dbt_runner/test_dbt_runner.py
index 20041f05952..40edcccae8d 100644
--- a/tests/functional/dbt_runner/test_dbt_runner.py
+++ b/tests/functional/dbt_runner/test_dbt_runner.py
@@ -23,6 +23,8 @@ def test_command_invalid_option(self, dbt: dbtRunner) -> None:
     def test_command_mutually_exclusive_option(self, dbt: dbtRunner) -> None:
         res = dbt.invoke(["--warn-error", "--warn-error-options", '{"include": "all"}', "deps"])
         assert type(res.exception) == DbtUsageException
+        res = dbt.invoke(["deps", "--warn-error", "--warn-error-options", '{"include": "all"}'])
+        assert type(res.exception) == DbtUsageException
 
     def test_invalid_command(self, dbt: dbtRunner) -> None:
         res = dbt.invoke(["invalid-command"])
diff --git a/tests/functional/defer_state/test_defer_state.py b/tests/functional/defer_state/test_defer_state.py
index 3a139f8aa47..102345fdf6e 100644
--- a/tests/functional/defer_state/test_defer_state.py
+++ b/tests/functional/defer_state/test_defer_state.py
@@ -5,7 +5,6 @@
 
 import pytest
 
-from dbt.cli.exceptions import DbtUsageException
 from dbt.contracts.results import RunStatus
 from dbt.exceptions import DbtRuntimeError
 from dbt.tests.util import run_dbt, write_file, rm_file
@@ -105,11 +104,6 @@ def run_and_save_state(self, project_root, with_snapshot=False):
 
 
 class TestDeferStateUnsupportedCommands(BaseDeferState):
-    def test_unsupported_commands(self, project):
-        # make sure these commands don"t work with --defer
-        with pytest.raises(DbtUsageException):
-            run_dbt(["seed", "--defer"])
-
     def test_no_state(self, project):
         # no "state" files present, snapshot fails
         with pytest.raises(DbtRuntimeError):
diff --git a/tests/unit/test_manifest.py b/tests/unit/test_manifest.py
index 8268e988361..5a2053e6f86 100644
--- a/tests/unit/test_manifest.py
+++ b/tests/unit/test_manifest.py
@@ -1019,7 +1019,7 @@ def test_build_flat_graph(self):
                 self.assertEqual(frozenset(node), REQUIRED_PARSED_NODE_KEYS)
         self.assertEqual(compiled_count, 2)
 
-    def test_add_from_artifact(self):
+    def test_merge_from_artifact(self):
         original_nodes = deepcopy(self.nested_nodes)
         other_nodes = deepcopy(self.nested_nodes)
 
@@ -1041,7 +1041,8 @@ def test_add_from_artifact(self):
 
         original_manifest = Manifest(nodes=original_nodes)
         other_manifest = Manifest(nodes=other_nodes)
-        original_manifest.add_from_artifact(other_manifest.writable_manifest())
+        adapter = mock.MagicMock()
+        original_manifest.merge_from_artifact(adapter, other_manifest.writable_manifest(), {})
 
         # new node added should not be in original manifest
         assert "model.root.nested2" not in original_manifest.nodes