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Core: Fix QUnit.module.only logic for unscoped modules

This bug affected use of QUnit.module.only when used in a "flat" way,
e.g. without scoping. For the following, it resulted in running test 1A and
2A, instead of only 1A:

```
QUnit.module.only( "Module one" );
QUnit.test( "1A", assert => { assert.ok( true ); } );

QUnit.module( "Module two" );
QUnit.test( "2A", assert => { assert.ok( false ); } );
```

Also move the "only" tests to CLI suite to verify TAP output
(more stable than `QUnit.done` post-run hack in HTML).

Fixes https://github.com/qunitjs/qunit/issues/1272.

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