[OfficialAbhinavSingh]

With the GitHub token now on the server, the PR gate picked up plan 5bbf7d86's request, then failed:

the change of task 1 does not apply: git failed: error: fulfilment/inventory.py: patch does not apply

All four tasks had passed. Task 1 depends on task 0.

Why. Each stored patch is git diff HEAD from a checkout of the plan's base. Before a dependent task runs, the worker applies its dependencies' patches (staged, not committed). So the dependent task's patch includes those changes again. The PR gate applies all patches in index order with a plain git apply, and that refuses the repeat.

Fix. Workspace.apply_patch now uses git apply --index --3way. A three-way merge sees the same change on both sides and takes it once. Two tasks that change the same lines differently still conflict and fail, as before. The worker applies dependency patches through the same method, so a task that depends on two tasks sharing a dependency no longer fails either.

Checks

• Two new tests use real git diff --binary patches. A dependent task's patch that repeats its dependency's change now combines (the test fails on main with the production error). Two different edits to one line still refuse.
• Replayed plan 5bbf7d86's actual stored patches against the sandbox repo:
  • plain apply: fails on task 1, the same as production;
  • --3way: all four apply, giving 2 files and +72 lines, and the repo's tests pass (58).
• ruff, ruff format and pyright clean. 561 unit tests and 13 Docker sandbox tests pass.

After this deploys, the PR on 5bbf7d86 can be retried from its run page.

Not in this PR

• The run page's change summary still adds up every task's patch, so it shows +168 for a +72 change. The diff endpoint concatenates the cumulative per-task patches.
• A dependent task's allowed_paths check also counts the files its dependencies changed. They're staged in its sandbox, not committed.