aube deploy doesn't preserve patches

[hilja]

Repro: https://github.com/hilja/aube-update-repro/tree/main/deploy

Correct me if I'm wrong, but if I run aube -F=foo deploy --prod deployed-foo in the above repro, the patch should be applied in deployed-foo/node_modules/is-even/index.js. But doesn't seem to be.

I was pulling my hair our earlier and realized I had to apply the patch manually in my docker, and then everything worked:

RUN git -C /app/node_modules/lighthouse apply /usr/src/app/patches/lighthouse@13.3.0.patch

[jdx]

Confirmed — this was a deploy bug, and #1213 fixes it.

aube deploy staged only the selected package files before running install from the standalone target. Workspace-root patchedDependencies metadata and patch files were therefore missing from that target, so install saw no patches and silently materialized the original dependency.

The fix resolves the source workspace patches before staging, copies them into each deploy target, and records equivalent patch metadata in the deployed manifest. I verified it against the linked reproduction: deployed-foo/node_modules/is-even/index.js now contains // PATCHED.

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