fix: keep nested assembly indexes consistent

[RanaPriyansh]

Nested assembly changes can leave Assembly.objects with missing paths or stale nodes. This addresses the nested index part of #2018. The requested find and list-based remove APIs remain separate.

Update only the added or removed receiver-relative paths in attached ancestors, and build copied indexes from copied children. This keeps ancestor paths, renamed copies, and detached subtrees consistent.

Validation:

• tests/test_assembly.py: 165 passed.
• Black accepted both changed files.
• Full suite: 896 passed, 3 skipped, 1 failed. The sole failure is the same test_interpPlate volume mismatch recorded on the unchanged baseline, so a full-suite pass is not claimed.

Codex used.

[RanaPriyansh]

Annotated the ancestor traversal variable as Optional[Assembly] so Mypy accepts its terminating None value.
Black and all 165 assembly tests pass locally.
The matching Mypy diagnostic is removed, but 165 unchanged local-environment errors remain, including missing OCP typing metadata.
The hosted rerun is pending.

Codex used.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.81%. Comparing base (c11b3f9) to head (41e30c3).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2102   +/-   ##
=======================================
  Coverage   95.80%   95.81%           
=======================================
  Files          30       30           
  Lines        9589     9606   +17     
  Branches     1439     1444    +5     
=======================================
+ Hits         9187     9204   +17     
  Misses        247      247           
  Partials      155      155           

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.