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Closes #11488. `pnpm fetch` writes forced-empty `hoistPattern: []` and `publicHoistPattern: []` into `.modules.yaml` (because its `virtualStoreOnly` install path skips hoisting). In v10 the follow-up `pnpm install` ignored these unless the user had explicitly set a hoist-pattern in their config. v11's [#11199](https://github.com/pnpm/pnpm/pull/11199) removed that explicit-config gate, so `validateModules` now always sees the empty patterns as a hoist-pattern change and purges `node_modules` — slow on every CI run, and per the bug report sometimes leaves the modules dir in an `ERR_MODULE_NOT_FOUND` state on subsequent runs. The fix marks `.modules.yaml` with a new `virtualStoreOnly: true` field after a fetch. `validateModules` recognizes this flag as "incomplete install state" and skips the `PUBLIC_HOIST_PATTERN_DIFF` / `HOIST_PATTERN_DIFF` comparisons. The next install then completes the missing post-import linking in place rather than purging. The flag is dropped from `.modules.yaml` once a normal install runs. A genuine hoist-pattern change (without a fetch in between) still triggers the purge as before — verified manually with `publicHoistPattern` in `pnpm-workspace.yaml`.