fix: Resolve all lockfile pruning test failures (#12009)
## Summary
- Fix Berry lockfile pruning to preserve `cacheKey` when the output
contains packages with checksums
- Fix NPM lockfile pruning to preserve the original `lockfileVersion`
instead of always forcing v3
- Regenerate all broken test fixtures with valid lockfiles while
preserving their edge cases
## Code changes
**`crates/turborepo-lockfiles/src/berry/mod.rs`**: The `lockfile()`
method was checking only `self.resolutions` for checksums to decide
whether to strip `cacheKey`. When a pruned subgraph's resolutions only
contained workspace references (no checksums), the key was incorrectly
dropped — even though the output packages map did contain npm packages
with checksums. Now checks the actual output packages instead.
**`crates/turborepo-lockfiles/src/npm.rs`**: `subgraph()` was hardcoding
`lockfile_version: 3` in the pruned output. This broke `npm ci` for
lockfileVersion 2 projects (npm@8). Now preserves the original version.
## Fixture changes
Many fixtures had fundamentally broken lockfiles (nonexistent npm
packages, fake integrity hashes, missing patch files, missing transitive
dependencies). These were regenerated with real package managers while
preserving the specific edge cases each fixture tests:
| Fixture | Edge case preserved |
|---|---|
| `berry` | `patch:` protocol for lodash via `resolutions` field |
| `berry_semver` | Major-only semver range (`"2"`) |
| `minimal-berry-resolutions` | Resolution override forcing
`debug@3.2.7` when workspace declares `^4.3.4` |
| `yarn4-resolution` | Resolution override pinning `react@18.2.0`
against `^18.2.0` range |
| `yarn4-catalog` | `catalog:` protocol with definitions in
`.yarnrc.yml` |
| `yarn4-patch` / `yarn4-direct-and-indirect` | Real `.yarn/patches/`
files for `is-odd` |
| `npm-lock-workspace-variation` | Object-form `workspaces: { packages:
[...] }` and differing lockfile/package name |
| `issue-10985` | Peer dep `next: ^14 \|\| ^15` with different resolved
versions per consumer |
## Testing
171/171 lockfile tests pass. 146/146 Rust unit tests pass.
