fix(vitest): fix file snapshots in skipped suites considered obsolete

[hi-ogawa]

Description

Closes #2442
Supersedes and closes #4009

Current behavior was quite tricky, so I created (hopefully) cleaner repro here (and this is the base of the test I added in this PR):

• https://stackblitz.com/edit/vitest-dev-vitest-xqw54j?file=repro.test.ts

The repro shows that treating snapshots as "obsolete" is not only about wrong warning, but also it has a consequence of deleting those skipped snapshots when running with -u.

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