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This is probably a bad idea to be doing this, but locally I don't see why it should cause an issue.
When I'm creating/editing/renaming query files while a script is importing data, sometimes my IDE creates temporary files in the same directory. When PhpStorm does this, it creates a sibling file called originalFileName.sql~
, and if a query is attempted to be run while this file exists, an exception is thrown.
It'd probably be a good idea to ignore file types that aren't recognised, if there's a matching file of a known type.