[Python] flatc --python silently overwrites existing __init__.py files #9229

flatc version: 25.12.19 (also older)
Generator: --python

What

flatc --python creates an empty __init__.py in every folder of the
namespace path. If one of those folders already has a hand-written
__init__.py with code in it, flatc replaces it with an empty file without warning.

Why

I wanted the generated files to live under my apps ipc folder which deals with the websocket server and the flatbuffer stuff

Repro

Project already has these real files:

src/myapp/__init__.py         # e.g. `def main(): ...`
src/myapp/ipc/__init__.py     # e.g. re-exports

schema/foo.fbs:

namespace myapp.ipc.generated;
table Thing { x: int; }

Run:

flatc --python -o src schema/foo.fbs

Now src/myapp/__init__.py and src/myapp/ipc/__init__.py are empty.
I found it happened through basedpyright lsp:
ImportError: cannot import name 'main' from 'myapp'.

Expected

flatc should not destroy source files it did not generate. Any of:

• don't touch an __init__.py in a folder that already exists
• never overwrite a non-empty __init__.py
• only write __init__.py for the innermost namespace folder
• add a flag like --python-no-init

Notes

• --gen-onefile skips the __init__.py chain but doesn't emit
  cross-schema imports, so it breaks for schemas that use include. Not a
  workaround.
• --ts is fine — it writes into a fresh tree and doesn't clobber
  hand-written files.
• flatc --help (25.12.19) has no flag to control __init__.py output.

Workarounds

1. Generate into a temp dir, move only the leaf namespace folder into place.
2. Give the generated code its own top-level package, with a namespace
   prefix no hand-written module shares.