docs(notes[plan]): Mark L1/L2/L3 resolved, fix stale line numbers, reorganize phases

why: libtmux#635 closed — all three API additions shipped in v0.55.0.
Line references drifted as code grew. Phase structure misrepresented
what's blocked vs unblocked.
what:
- Mark L1, L2, L3 as RESOLVED with correct libtmux source locations
- Fix 20+ stale line number references across importers.py, builder.py, libtmux
- Move T2 from Phase 3 to Phase 2, mark Phase 3 COMPLETE
- Move T9 to Phase 5 as unblocked, remove L2/L3 from Phase 5
- Fix EnvironmentMixin location (common.py, not session.py)

Author: tony