Fix tests

[guilhas07]

fix(test): normalize no-sort/no-bundle option handling in test runner

Problem:

1. sort and bundle were unconditionally derived from no-sort/no-bundle,
   ignoring explicit sort/bundle values set directly in options.yaml
2. The no-bundle delete guard incorrectly checked no-sort as its first
   condition.

Solution:

Default sort and bundle to true, and only translate the no-X keys when they
are actually present in the options file.

Test

To test, with the other fix applied, after a destroyOutput=true run:
npx jest bin/cli.test.js --no-coverage -t "should not bundle reference"

fix(test): destroyOutput regeneration double serialization and output file mutation

Problem:

When running with destroyOutput set the following problems arise:

1. test/test.js called writeFile(outputFilename, result, options) where result is already
   a serialized string returned by run(), effectivelly double encoding it.
   The next test run (npx jest test/test.js) would load this corrupted content as the
   expected snapshot, causing all JSON test cases in test.js to fail.

2. test/utils/test-utils.js loadTest() ran the CLI without overriding --output, so the
   CLI used the output path from options.yaml. Which during a run with
   deleteOutput set, would silently overwrite and mask
   the corruption from (1) while still producing test failures.

Solution:

• Write the already-serialized result string directly with fs.writeFileSync in test.js.
• Pass --output in loadTest so the CLI writes to a temp file instead of the
  shared output. Output file mutation is now exclusive owned by test.js.

[thim81]

@guilhas07 Great of you to figure out the quirky behaviour in the tests suite.
It has been around for such a long time, and I knew there was something strange with but I never figured out what was actually causing it.

Thank you for taking the time to fix it with this PR 👏