Duplicate module silently replaces existing module in dmypy recheck --update

If one has these two files:

# [file a/mod.py]
# empty

# [file b/mod.py]
42 + 'no'

and there are no __init__.py[i] files in the directories, then running dmypy produces the following result:

$ dmypy start -- --follow-import=skip
Daemon started
$ dmypy check a/mod.py 
$ dmypy recheck --update b/mod.py
b/mod.py:1: error: Unsupported operand types for + ("int" and "str")
$ dmypy recheck --remove b/mod.py
b/mod.py:1: error: Unsupported operand types for + ("int" and "str")
$ dmypy recheck --update a/mod.py
b/mod.py:1: error: Unsupported operand types for + ("int" and "str")

The problem here is twofold:

• When we first trying to add the duplicate module, this should cause a blocking error, as in normal/incremental run instead of silently replacing the other module.
• Even after one tries to remove the problematic module, it stays in build causing errors in all subsequent runs independently of what is done (except just stopping the daemon).

This is high priority because it causes troubles when adding files in existing large codebases.

Riproduci la sequenza con dmypy start, check, recheck --update, recheck --remove e recheck --update usando i due file mod.py duplicati. Traccia il modo in cui il daemon gestisce i moduli duplicati durante l’aggiornamento e la rimozione. Il lavoro è completato quando l’aggiunta del duplicato segnala un errore bloccante, la sua rimozione elimina il modulo obsoleto e le verifiche successive non segnalano più il relativo errore.