🐛 fix(config): set_env file| no longer overrides later values

[gaborbernat]

When set_env mixes file| references with inline variable definitions, values from the env file always took precedence regardless of ordering. This broke the intuitive "last definition wins" rule that works correctly for purely inline definitions.

[testenv]
set_env =
    file|.env       # .env contains FOO=BAR
    FOO=QUX         # expected QUX, got BAR

🔧 The fix tracks which keys are defined after each file| reference during parsing, then skips those keys when loading the env file. Variables only defined in the file still come through normally, while explicit inline overrides now take precedence as expected.

⚠️ Users who relied on env file values silently overriding later inline definitions will see changed behavior. The new behavior matches the principle of least surprise — definitions appearing later in the config win.

Fixes #3335