Add stage rollback and stale downstream tracking

[Zefan-Cai]

Summary

This PR isolates TODO 2 from the larger CLI branch: add explicit cross-stage rollback and downstream stale invalidation on top of zefan-todo-1.

What Changed

• added --rollback-stage CLI support
• added manifest-level rollback support via rollback_to_stage(...)
• marks the rollback target stage as pending/dirty
• marks downstream stages as stale
• rebuilds approved memory from the manifest after rollback
• added a focused regression test in tests/test_stage_rollback.py

Base

• base branch: zefan-todo-1

Scope

This PR is intentionally limited to TODO 2 only.

Not included here:

• operator session recovery hardening
• stage handoff / context compression
• paper/release package generation

Validation

• python -m py_compile main.py src/*.py tests/*.py
• python -m unittest tests.test_stage_rollback tests.test_run_manifest tests.test_writing_pipeline -v