Crash when packages and mypy_path discover one file under two module names

[elprans]

Mypy crashes while reporting an ordinary type error when one physical package is discovered under two configured package roots. The existing duplicate-module diagnostic does not catch this packages + mypy_path configuration.

Minimal reproduction

Directory layout:

pyproject.toml
src/
  outer/
    __init__.py
    inner/
      example/
        __init__.py
        module.py

pyproject.toml:

[tool.mypy]
python_version = "3.14"
strict = true
mypy_path = ["src", "src/outer/inner"]
packages = ["outer", "example"]
explicit_package_bases = true

src/outer/inner/example/module.py:

def takes_int(value: int) -> None:
    pass


def broken() -> None:
    takes_int("not an int")

The __init__.py files are empty.

$ uv run --no-project --with mypy==2.3.1 mypy --no-incremental --show-traceback
src/outer/inner/example/module.py:6: error: Argument 1 to "takes_int" has incompatible type "str"; expected "int"  [arg-type]
.../src/outer/inner/example/module.py:6: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 2.3.1
.../src/outer/inner/example/module.py:6: note: use --pdb to drop into pdb
Traceback (most recent call last):
  File "mypy/checkexpr.py", line 6163, in accept
  File "mypy/checkexpr.py", line 499, in visit_call_expr
  File "mypy/checkexpr.py", line 630, in visit_call_expr_inner
  File "mypy/checkexpr.py", line 1498, in check_call_expr_with_callee_type
  File "mypy/checkexpr.py", line 1591, in check_call
  File "mypy/checkexpr.py", line 1873, in check_callable_call
  File "mypy/checkexpr.py", line 2762, in check_argument_types
  File "mypy/checkexpr.py", line 2799, in check_arg
  File "mypy/messages.py", line 812, in incompatible_argument
  File "mypy/messages.py", line 282, in fail
  File "mypy/messages.py", line 260, in report
  File "mypy/errors.py", line 680, in report
  File "mypy/errors.py", line 810, in add_error_info
  File "mypy/errors.py", line 684, in _add_error_info
    assert file not in self.flushed_files
AssertionError

Expected: report the ordinary arg-type error once, or reject the duplicate physical-file/module-name mapping with a useful diagnostic. Mypy should not crash.

This also reproduces on current master d32c4d38770745dd9fb6a0279204425e6070e6ad (2.4.0+dev.d32c4d).

Environment

• macOS arm64
• Python 3.14.7
• mypy 2.3.1 compiled wheel

Prior issue search

This seems to be a similar underlying duplicate-file condition as #4881 and #7510, but both are closed because mypy added a "Source file found twice under different module names" diagnostic. That diagnostic does not prevent this configuration-driven variant in 2.3.1 or current master.

AI Disclosure

gpt-5.6-sol used to synthesize the minimal reproducer. I've reproduced this manually.