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.

Reproduce the sequence with dmypy start, check, recheck --update, recheck --remove, and recheck --update using the two duplicate mod.py files. Trace how the daemon handles duplicate modules during update and removal. Done means adding the duplicate reports a blocking error, removing it clears the stale module, and later rechecks no longer report its error.