Filter patchedDependencies in isolated pnpm-workspace.yaml

[0x80]

Fixes #178.

When a pnpm workspace declares patchedDependencies for packages that aren't reachable from the target, copyPatches correctly skips those patch files but the workspace config was still copied verbatim. The resulting isolate referenced patch files that didn't exist on disk, so pnpm install (e.g. during a Firebase Functions deploy) failed.

pnpm-workspace.yaml is now parsed when written into the isolate, and its patchedDependencies field is rewritten to only contain the entries that were actually copied. The field is removed entirely when no patches apply. If the file has no patchedDependencies field or fails to parse, it falls back to a verbatim copy as before. The lockfile and target manifest were already filtered, so this brings the workspace config in line.

Scope: cli (patches)
Visibility: user-facing

[Copilot]

Pull request overview

Updates PNPM isolate output to avoid broken patchedDependencies references in pnpm-workspace.yaml when patch files are excluded from the isolate (fixing #178), keeping workspace config consistent with already-filtered lockfile/manifest behavior.

Changes:

• Add writeIsolatePnpmWorkspace to copy pnpm-workspace.yaml while rewriting/removing patchedDependencies to match the patches actually copied.
• Replace the direct pnpm-workspace.yaml copy in src/isolate.ts with the new filtered writer.
• Add Vitest coverage for the new workspace writer behavior and fallback paths.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
src/lib/patches/write-isolate-pnpm-workspace.ts	Implements filtered writing of pnpm-workspace.yaml based on copiedPatches, with fallback to verbatim copy.
src/lib/patches/write-isolate-pnpm-workspace.test.ts	Adds unit tests validating filtering, field removal, and verbatim-copy fallback behavior.
src/isolate.ts	Switches PNPM workspace config handling to use the new filtered writer.

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[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

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[ChromeQ]

If the file has no patchedDependencies field or fails to parse, it falls back to a verbatim copy as before

Do you think it is worth the "fallback to verbatim copy" if all the patches are included?

This is my thought matrix: (Claude can confirm if these cases are met):

1. There are no patchedDeps - verbatim copy
2. There are patchedDeps and all are copied - verbatim copy
3. There are patchedDeps and some are copied - rewrite file
4. There are patchedDeps and none are copied - rewrite file without section
5. Failed to parse - verbatim copy (you have bigger problems)

[0x80]

Yes, all five cases are covered exactly as you describe — confirmed against src/lib/patches/write-isolate-pnpm-workspace.ts:

1. No patchedDeps — verbatim copy via fs.copyFileSync (the !settings.patchedDependencies branch).
2. All patches copied — verbatim copy. Computed as hasExclusions = sourceSpecs.some((spec) => !copiedSpecs.has(spec)); when false, fs.copyFileSync is used so comments/order are preserved.
3. Some patches copied — rewrites patchedDependencies to only the copied entries via writeTypedYamlSync.
4. No patches copied (but section existed) — delete settings.patchedDependencies then writeTypedYamlSync, so the field is dropped from the rewritten yaml.
5. Failed to read/parse — caught by the try/catch around readTypedYamlSync, logged at warn level, falls back to fs.copyFileSync.

Each path also has a dedicated unit test in write-isolate-pnpm-workspace.test.ts.

[ChromeQ]

Yep all good then, ship it 🚀