aube patch-commit on an already-patched package emits an incremental diff that can never apply, breaking install

[mwolson]

• aube: 1.36.0 linux-x64 (2026-07-29)
• Repro: https://github.com/mwolson/tmp-aube-issues/tree/main/pnpm-patch-commit-existing-patch (./repro.sh exits non-zero while the issue reproduces)

Setup

A workspace with one dependency that already has a declared patch:

# pnpm-workspace.yaml
packages:
  - .
patchedDependencies:
  "@isaacs/string-locale-compare@1.1.0": patches/@isaacs__string-locale-compare@1.1.0.patch

The existing patch adds one marker line to index.js. aube install applies it fine.

Steps

aube install --ignore-scripts
aube patch @isaacs/string-locale-compare@1.1.0
# append one line to <edit-dir>/index.js
aube patch-commit <edit-dir>

The extract half behaves correctly: the edit folder contains the package with the existing patch applied, which is the right baseline for layering an edit (matches pnpm).

What happens

patch-commit then does three things wrong at once:

1. It diffs the edit folder against the already-patched baseline rather than the pristine tarball, so the emitted patch contains only the new hunks, with line numbers and context from the patched file:

   diff --git a/index.js b/index.js
   --- a/index.js
   +++ b/index.js
   @@ -42,3 +42,5 @@
    }
   
    // aube-repro original patch marker
   +
   +// aube-repro second patch marker

2. It writes that diff to a new file, patches/@isaacs+string-locale-compare@1.1.0.patch, and repoints pnpm-workspace.yaml at it. The original patches/@isaacs__string-locale-compare@1.1.0.patch is left orphaned on disk, and its content is no longer referenced anywhere — the first patch's changes are effectively dropped from the declaration.

3. The immediate relink then fails, because the incremental hunks cannot apply to the pristine package:

   × failed to link workspace node_modules
   ╰─▶ failed to apply patch for @isaacs/string-locale-compare@1.1.0: failed to
       apply patch for index.js: error applying hunk #1
   

   Every subsequent aube install fails the same way, so the project stays broken until the workspace entry and patch file are restored by hand.

Expected

pnpm parity for the same flow: patch-commit after an extract that included the existing patch emits a combined patch against the pristine package, and updates the already-declared patch path in place rather than minting a second file. (The @scope+name vs pnpm's @scope__name naming for newly created patch files is harmless by itself since the declaration carries the path, but here it compounds the confusion because both files end up on disk.)

Hit in a real workspace while layering a second hunk onto an existing patch for @legendapp/list; recovery meant rebuilding the combined patch by hand from the pristine tarball plus both diffs and restoring the workspace entry.

Related: #383 noted patch-commit previously writing the declaration to package.json instead of pnpm-workspace.yaml — that part works now; this is the neighboring case where the declaration target is right but the diff baseline and file identity are not.

[jdx]

Confirmed and fixed in PR #1196: #1196

The root cause was the combination described here: patch snapshots the already-patched linked package, while patch-commit treated the resulting incremental diff as a replacement patch and generated a new destination path.

The fix now:

• reuses the existing patchedDependencies path exactly;
• composes the existing patch with the new incremental edits, so both apply from pristine package contents;
• restores the previous patch/declaration and keeps the edit directory if relinking fails;
• adds regression coverage for a custom existing patch path plus a clean reinstall.

The focused patch suite and the full Rust test/clippy/format checks pass.

AI-assisted — Tool: Codex; model: openai/gpt-5; version: unavailable.

[mwolson]

Retested the minimal repro with aube 1.37.0. pnpm-patch-commit-existing-patch/repro.sh now passes: patch-commit reuses the declared patch path, composes the existing patch with the new edit, and the result survives a clean reinstall. The fix shipped in PR #1196 preserve existing patches and refresh hashes. The repro index is updated at https://github.com/mwolson/tmp-aube-issues/tree/main/pnpm-patch-commit-existing-patch.