mach: fix logic to override paths for legacy layout (#34467)

wptrunner internally derives the path to the MANIFEST.json file from the
`metadata_path` passed via `test_paths`. The current logic overrides
only the `metadata_path`, leaving the manifest_path pointing at the
wrong (non-legacy) layout's MANIFEST.json.

In #34436 we observed that the recent WPT imports create a transient
`.cache` diretory that wptrunner logic uses for optimization. This has
not been observed until #34436 because a [recent bump in MANIFEST.json's
schema version][1] triggered the creation of the cache. Because of the
above issue with incorrect path and the fact that we *first* trigger
`mach update-wpt` for legacy layout during WPT import, the MANIFEST.json
of non-legacy layout gets incorrectly migrated during the invocation of
`update-wpt` for legacy layout but the cache is still created under
legacy-layout's path as it is not based on `manifest_path`. The
subsequent invocation of `mach update-wpt` for non-legacy finds the
MANIFEST.json already migrated so the `.cache` directory is not
constucted.

This change simply replaces the whole object using the wptrunner's
`TestRoot` class constructor so that all derived paths are calculated
correctly. We also add the `.cache` folders to gitignore as it seems
like they are expected to be created during such version migrations.

[1]: https://github.com/web-platform-tests/wpt/pull/49406

Signed-off-by: Mukilan Thiyagarajan <mukilan@igalia.com>

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