Fix flatten refs recursive

[tvt173]

I noticed a bug in the new flatten_invalid_refs_recursive function which caused some refs to drop. While debugging, I realized there is also a bug in the setter of ComponentReference.parent and also ref_cell, that the actual gdstk cell does not update when you set it to something new. This MR fixes both of those issues.

[sourcery-ai]

Sourcery Code Quality Report

✅  Merging this PR will increase code quality in the affected files by 1.40%.

Quality metrics	Before	After	Change
Complexity	6.01 ⭐	5.57 ⭐	-0.44 👍
Method Length	62.65 🙂	60.82 ⭐	-1.83 👍
Working memory	7.79 🙂	8.02 🙂	0.23 👎
Quality	67.16% 🙂	68.56% 🙂	1.40% 👍

Other metrics	Before	After	Change
Lines	3144	3117	-27

Changed files	Quality Before	Quality After	Quality Change
gdsfactory/component.py	64.87% 🙂	66.58% 🙂	1.71% 👍
gdsfactory/component_reference.py	72.66% 🙂	73.11% 🙂	0.45% 👍

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
gdsfactory/component.py	Component._write_library	20 😞	356 ⛔	18 ⛔	23.01% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
gdsfactory/component_reference.py	ComponentReference.move	15 🙂	280 ⛔	15 😞	31.99% 😞	Try splitting into smaller methods. Extract out complex expressions
gdsfactory/component.py	Component.plot_holoviews	14 🙂	475 ⛔	12 😞	33.50% 😞	Try splitting into smaller methods. Extract out complex expressions
gdsfactory/component.py	Component.add_polygon	18 🙂	282 ⛔	12 😞	33.79% 😞	Try splitting into smaller methods. Extract out complex expressions
gdsfactory/component.py	Component.remap_layers	29 😞	216 ⛔	10 😞	33.89% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions

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• 🙂 good
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• ⛔ very poor

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[codecov]

Codecov Report

Merging #1258 (aadbb52) into main (6c3d6cd) will increase coverage by 0.46%.
The diff coverage is 87.80%.

@@            Coverage Diff             @@
##             main    #1258      +/-   ##
==========================================
+ Coverage   68.75%   69.22%   +0.46%     
==========================================
  Files         356      356              
  Lines       21150    21177      +27     
  Branches     3038     3044       +6     
==========================================
+ Hits        14542    14659     +117     
+ Misses       5752     5633     -119     
- Partials      856      885      +29     

Impacted Files	Coverage Δ
gdsfactory/component.py	67.99% <87.09%> (-0.27%)	⬇️
gdsfactory/component_reference.py	75.19% <90.00%> (+0.46%)	⬆️
gdsfactory/write_cells.py	72.94% <0.00%> (-5.54%)	⬇️
gdsfactory/pdk.py	55.32% <0.00%> (ø)
gdsfactory/klive.py	68.42% <0.00%> (ø)
gdsfactory/components/__init__.py	100.00% <0.00%> (ø)
gdsfactory/show.py	50.00% <0.00%> (+2.94%)	⬆️
gdsfactory/components/disk.py	81.25% <0.00%> (+5.57%)	⬆️
gdsfactory/routing/all_angle.py	26.33% <0.00%> (+18.30%)	⬆️
... and 1 more

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[joamatab]

Thank you Troy!

[joamatab]

just released v6.36.0