Use two-phase type checking in sequential mode

[ilevkivskyi]

Fixes #21348

This means that (unless local partial types are disabled) we should have identical semantics for all three: sequential (in-process) type-checking, parallel type-checking, and in the daemon.

When reading the relevant code I noticed a bug, when using -c in parallel mode we do not check implementations in the code passed with -c, fix is quite simple (just reorder writing cache and flushing the errors), so I simply add it here.

cc @JukkaL

[github-actions]

Diff from mypy_primer, showing the effect of this PR on open source code:

steam.py (https://github.com/Gobot1234/steam.py)
- steam/chat.py:248: error: "fetch_message_reactors" of "ConnectionState" gets multiple values for keyword argument "server_timestamp"  [misc]
- steam/chat.py:248: error: "fetch_message_reactors" of "ConnectionState" gets multiple values for keyword argument "ordinal"  [misc]
- steam/chat.py:248: error: "fetch_message_reactors" of "ConnectionState" gets multiple values for keyword argument "reaction_name"  [misc]
- steam/chat.py:248: error: "fetch_message_reactors" of "ConnectionState" gets multiple values for keyword argument "reaction_type"  [misc]
- steam/chat.py:290: error: Too many arguments for "react_to_chat_message" of "ConnectionState"  [call-arg]
- steam/chat.py:290: error: "react_to_chat_message" of "ConnectionState" gets multiple values for keyword argument "reaction_type"  [misc]
- steam/chat.py:290: error: "react_to_chat_message" of "ConnectionState" gets multiple values for keyword argument "is_add"  [misc]
- steam/chat.py:318: error: Too many arguments for "ack_chat_message" of "ConnectionState"  [call-arg]

spark (https://github.com/apache/spark)
+ python/pyspark/pandas/frame.py:666: error: Unused "type: ignore" comment  [unused-ignore]
+ python/pyspark/pandas/frame.py:666: error: Redundant cast to "InternalFrame"  [redundant-cast]
+ python/pyspark/pandas/frame.py:666: note: Error code "redundant-cast" not covered by "type: ignore[has-type]" comment
+ python/pyspark/streaming/context.py:226: error: Incompatible types in assignment (expression has type "StreamingContext", variable has type "None")  [assignment]

prefect (https://github.com/PrefectHQ/prefect)
+ src/prefect/runner/runner.py:329: error: Incompatible return value type (got "EventsClient | None", expected "EventsClient")  [return-value]
- src/prefect/runner/runner.py:306: error: Cannot determine type of "_scheduled_run_poller"  [has-type]
- src/prefect/runner/runner.py:312: error: Cannot determine type of "_scheduled_run_poller"  [has-type]
- src/prefect/runner/runner.py:329: error: Cannot determine type of "_event_emitter"  [has-type]
- src/prefect/runner/runner.py:670: error: Cannot determine type of "_scheduled_run_poller"  [has-type]
- src/prefect/runner/runner.py:672: error: Cannot determine type of "_scheduled_run_poller"  [has-type]
- src/prefect/runner/runner.py:686: error: Cannot determine type of "_cancellation_manager"  [has-type]
- src/prefect/runner/runner.py:698: error: Cannot determine type of "_scheduled_run_poller"  [has-type]
- src/prefect/runner/runner.py:699: error: Cannot determine type of "_scheduled_run_poller"  [has-type]
- src/prefect/runner/runner.py:796: error: Cannot determine type of "_runs_task_group"  [has-type]
- src/prefect/runner/runner.py:1243: error: Cannot determine type of "_cancellation_manager"  [has-type]
- src/prefect/runner/runner.py:1360: error: Cannot determine type of "_event_emitter"  [has-type]
- src/prefect/runner/runner.py:1368: error: Cannot determine type of "_event_emitter"  [has-type]

operator (https://github.com/canonical/operator)
- ops/lib/__init__.py:86: error: "None" has no attribute "get"  [attr-defined]
+ ops/lib/__init__.py:86: error: Item "None" of "Any | None" has no attribute "get"  [union-attr]

altair (https://github.com/vega/altair)
+ altair/vegalite/v6/api.py:3997: error: Argument "spec" to "FacetChart" has incompatible type "_EncodingMixin"; expected "SchemaBase | Mapping[str, Any] | UndefinedType"  [arg-type]

egglog-python (https://github.com/egraphs-good/egglog-python)
+ python/egglog/builtins.py:259: error: Unused "type: ignore" comment  [unused-ignore]
+ python/egglog/builtins.py:266: error: Unused "type: ignore" comment  [unused-ignore]
+ python/egglog/builtins.py:370: error: Unused "type: ignore" comment  [unused-ignore]
+ python/egglog/builtins.py:377: error: Unused "type: ignore" comment  [unused-ignore]
+ python/egglog/builtins.py:840: error: Unused "type: ignore" comment  [unused-ignore]
+ python/egglog/builtins.py:847: error: Unused "type: ignore" comment  [unused-ignore]
+ python/egglog/builtins.py:967: error: Unused "type: ignore" comment  [unused-ignore]
+ python/egglog/builtins.py:973: error: Unused "type: ignore" comment  [unused-ignore]

pip (https://github.com/pypa/pip)
+ src/pip/_internal/resolution/resolvelib/candidates.py:410: error: Incompatible types in assignment (expression has type "Version", variable has type "None")  [assignment]
+ src/pip/_internal/resolution/resolvelib/candidates.py:411: error: Incompatible return value type (got "None", expected "Version")  [return-value]

pandera (https://github.com/pandera-dev/pandera)
- pandera/engines/polars_engine.py:270: error: "type[object]" has no attribute "to_schema"  [attr-defined]
+ pandera/api/pandas/array.py:38: error: Unused "type: ignore" comment  [unused-ignore]

sympy (https://github.com/sympy/sympy)
+ sympy/matrices/matrixbase.py:3319: error: Unused "type: ignore" comment  [unused-ignore]

trio (https://github.com/python-trio/trio)
+ src/trio/_dtls.py:739: error: Incompatible types in assignment (expression has type "tuple[bytes, bytes]", variable has type "None")  [assignment]

jax (https://github.com/google/jax)
- jax/_src/array.py:409: error: No overload variant of "asarray" matches argument types "ndarray[tuple[Any, ...], dtype[Any]]", "dtype[Any] | None", "dict[str, bool]"  [call-overload]
+ jax/_src/array.py:409: error: No overload variant of "asarray" matches argument types "Any", "dtype[Any] | None", "dict[str, bool]"  [call-overload]

git-revise (https://github.com/mystor/git-revise)
+ gitrevise/odb.py:413: error: Redundant cast to "bytes"  [redundant-cast]