Verify canary release

• I verified that the issue exists in the latest Turborepo canary release.

Link to code that reproduces this issue

https://github.com/nzapponi/turbo-prune-bun-repro

Which canary version will you have in your reproduction?

2.5.3-canary.0

Environment information

turbo 2.5.3-canary.0

CLI:
   Version: 2.5.3-canary.0
   Path to executable: /Users/xxx/Desktop/bun-turbo-prune/node_modules/turbo-darwin-arm64/bin/turbo
   Daemon status: Not running
   Package manager: bun

Platform:
   Architecture: aarch64
   Operating system: macos
   WSL: false
   Available memory (MB): 3031
   Available CPU cores: 10

Environment:
   CI: None
   Terminal (TERM): xterm-256color
   Terminal program (TERM_PROGRAM): vscode
   Terminal program version (TERM_PROGRAM_VERSION): 1.99.2
   Shell (SHELL): /bin/zsh
   stdin: false

Expected behavior

Pruned lockfile should only include packages that are part of the dependencies of the given package.

Actual behavior

Pruned lockfile (https://github.com/nzapponi/turbo-prune-bun-repro/blob/dd539884f62e912c09f5f2ceed7ad28a663ef789/out/json/bun.lock) includes packages that shouldn't be in there (e.g. @react-native/community-cli-plugin/debug).

Because it includes it, bun install --frozen-lockfile fails.

To Reproduce

• Copy out/json folder outside the tree, remove bun.lock and run bun install
• Compare newly generated bun.lock with the one in my repo

Additional context

In the repro repo, bun install --frozen-lockfile still seems to succeed somehow, however in my larger private repo, I can't use --frozen-lockfile at all