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Prune causes breakage of boundaries #10547

@MoreRustLessAccess

Description

@MoreRustLessAccess

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/MoreRustLessAccess/turbo-prune-repro

Which canary version will you have in your reproduction?

turbo 2.5.4-canary.1

Environment information

turbo 2.5.4-canary.1

CLI:
   Version: 2.5.4-canary.1
   Path to executable: /workspaces/turbo-prune-repro/node_modules/.pnpm/turbo-linux-64@2.5.4-canary.1/node_modules/turbo-linux-64/bin/turbo
   Daemon status: Running
   Package manager: pnpm

Platform:
   Architecture: x86_64
   Operating system: linux
   WSL: false
   Available memory (MB): 6290
   Available CPU cores: 2

Environment:
   CI: None
   Terminal (TERM): xterm-256color
   Terminal program (TERM_PROGRAM): vscode
   Terminal program version (TERM_PROGRAM_VERSION): 1.100.3
   Shell (SHELL): /bin/bash
   stdin: false

Expected behavior

Turbo prune should leave the deny value not present

Actual behavior

Turbo makes the deny value null, causing all turbo commands to fail due to invalid config

To Reproduce

turbo ls # This works
turbo prune app-a
cd out
turbo ls # This fails

Additional context

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