[P2-worktree] Re-enable worktree isolation with real merge-back (+auto-commit, workspace_path, verify)

[frankbria]

Context

#714 [P0.3] shipped the sanctioned interim: --isolation worktree is hard-rejected so it can no longer silently discard agent work. This issue tracks re-implementing worktree isolation correctly and re-enabling it.

Why it wasn't done in #714

Real merge-back is entangled and unsafe to ship alone:

1. Uncommitted work — adapters run in the worktree but never git commit, so git merge cf/<task_id> merges nothing. Merge-back needs an auto-commit step in the worktree first.
2. #715 [P0.4] — the default react/builtin engine ignores workspace_path and writes to the main repo, so isolation is a no-op there until that's fixed.
3. #716 [P0.5] — VerificationWrapper runs gates against the main repo, not the worktree, so a worktree run would falsely pass.

Acceptance criteria

• After a successful worktree run: uncommitted changes are auto-committed on cf/<task_id>, then merge_back() merges to the base branch before cleanup.
• Merge conflict → surfaced as a blocker; the branch/worktree are preserved (not force-deleted) for recovery.
• Run failure/blocked → branch preserved (no git branch -D).
• validate_isolation() no longer rejects WORKTREE; the CLI re-accepts --isolation worktree.
• Integration test: a file created by the adapter under --isolation worktree exists on the base branch after a successful run.
• Regression test: a conflicting change produces a blocker and preserves the branch.

Dependencies

• blocked by [P0.4] Builtin (react/plan) engines ignore the worktree workspace_path — isolation is a silent no-op #715 (P0.4 — builtin engines must use the worktree path)
• blocked by [P0.5] VerificationWrapper runs gates/quick-fixes against the main repo, not the worktree the agent modified #716 (P0.5 — verification must run against the worktree)
• re-enables the path gated off in [P0.3] Worktree isolation must not silently discard external-engine work (merge_back is dead code) #714

Evidence / anchors

• codeframe/core/sandbox/context.py — validate_isolation() / create_execution_context() (WORKTREE branch to restore)
• codeframe/core/worktrees.py — TaskWorktree.merge_back() (implemented, currently unwired)
• codeframe/core/runtime.py:~931 — finally: exec_ctx.cleanup() (must merge before cleanup)

[coderabbitai]

🔗 Related PRs

#439 - feat(core): continuous reconciliation during batch execution [merged]
#441 - feat(core): worktree-per-task isolation for parallel batch execution [merged]
#536 - feat(core): ExecutionContext abstraction for task isolation (#532) [merged]
#537 - feat(core): WorktreeRegistry, orphan cleanup, and get_base_branch (#533) [merged]
#541 - feat(core): absorb parallel-cc worktree + E2B into CodeFrame namespace (#535) [merged]

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[frankbria]

Scope update: #715 (P0.4 — builtin engines thread workspace_path) and #716 (P0.5 — verification runs against the worktree) were closed as resolved-by-#714 (their bugs are unreachable while worktree is disabled). Their real work is folded into this issue. Updated checklist for re-enabling worktree correctly:

• Auto-commit uncommitted worktree changes before merge_back
• merge_back() on success → conflict-to-blocker → preserve branch on failure
• (from [P0.4] Builtin (react/plan) engines ignore the worktree workspace_path — isolation is a silent no-op #715) Builtin react/plan adapters thread workspace_path into ReactAgent/tool+lint execution; batch worktree path passes the workspace root explicitly (not via cwd)
• (from [P0.5] VerificationWrapper runs gates/quick-fixes against the main repo, not the worktree the agent modified #716) VerificationWrapper runs gates + quick-fixes against the workspace_path argument, not self._workspace.repo_path
• Remove the validate_isolation WORKTREE reject + restore the CLI/create_execution_context path
• Integration test: file created by an adapter under --isolation worktree exists on the base branch after a successful run; a conflicting change → blocker + preserved branch

Dependencies: none remaining (#715/#716 closed). This is now the single 'make worktree isolation actually work' issue.

[frankbria]

Reprioritized P0→P2: worktree isolation is now safely disabled (#714), so re-enabling this opt-in feature is a post-launch enhancement, not a beta blocker. Retitled to stop it sorting ahead of true P0 launch blockers.