Use shx for building packages

[OlSu11]

Use shx in order to build blocks on Windows machines

[gemini-code-assist]

Summary of Changes

Hello @OlSu11, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request enhances the project's build system by introducing the shx utility, which provides cross-platform compatible shell commands. This change primarily addresses issues with build scripts on Windows environments, ensuring a more consistent development experience across different operating systems without altering the core logic of the build steps.

Highlights

• Cross-platform Compatibility: Replaced direct rm and mv commands with shx rm and shx mv in various package.json scripts to ensure build processes function correctly on Windows machines.
• Dependency Management: Added shx as a development dependency in the root package.json and to the pnpm-workspace.yaml catalog, along with updating pnpm-lock.yaml to include shx and its transitive dependencies.
• Build Process Standardization: Standardized file removal and movement operations across multiple package build scripts (block, software/parse-h5ad, software/parse-seurat, workflow) using shx.

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[gemini-code-assist]

Code Review

This pull request correctly replaces Unix-specific shell commands with shx to ensure cross-platform compatibility for build scripts, particularly on Windows. The changes are applied consistently across all relevant packages. However, the introduction of the shx dependency also brings in a transitive dependency with a known security vulnerability. I have left a comment detailing the vulnerability and a recommended mitigation.

[gemini-code-assist]

Adding shx introduces a transitive dependency on minimist@1.2.8, which is vulnerable to Prototype Pollution (CVE-2021-44906). This could potentially be exploited if command-line arguments are crafted in a specific way.

To mitigate this, you should force pnpm to use a patched version of minimist by adding an override to your root package.json file.

"pnpm": {
  "overrides": {
    "minimist": ">=1.2.9"
  }
}

After adding this, run pnpm install to update your lockfile.