Integrate approved task patches with a safe three-way merge

[RomanEmreis]

Problem

Ferrus currently integrates an approved task with:

git apply --whitespace=nowarn PATCH.diff

Parallel tasks are built from pinned baseline trees. After one task changes a shared file, another task can fail with integration_error even when Git could merge its changes cleanly against the updated canonical workspace.

A literal switch to git apply --3way is not sufficient because it may update the Git index and may leave conflict stages or conflict markers. The current rollback path, git apply -R PATCH.diff, also cannot reliably restore the pre-integration workspace after a three-way merge.

Goal

Integrate approved task changes with a safe three-way workflow using:

• base: the task baseline tree
• ours: the exact current canonical workspace state
• theirs: the frozen submitted tree

Non-overlapping changes to the same file should merge automatically. Genuine conflicts should remain recoverable integration errors.

Requirements

• Preserve pre-existing canonical staged, unstaged, and untracked changes.
• Run three-way integration through an isolated worktree or temporary Git index.
• Do not leave conflict markers or unmerged index entries after failure.
• Restore the exact pre-attempt canonical state when integration fails.
• Restore the exact pre-attempt canonical state when post-apply checks fail.
• Keep the existing approval lock and source identity validation semantics.
• Continue writing a bounded INTEGRATION_ERROR.md for genuine conflicts.

Tests

• Two tasks changing different hunks of the same tracked file merge successfully.
• Overlapping changes produce integration_error.
• A failed merge leaves the canonical worktree and index unchanged.
• Failed post-apply checks restore the exact canonical state after a successful three-way merge.
• Existing staged, unstaged, untracked, binary, added, and deleted paths remain correct.