Propagate latest changes to autograd CM

[daquinteroflex]

Greptile Summary

This PR propagates autograd component modeler (CM) changes across the Tidy3D repository by updating submodules, refactoring code organization, and integrating autograd web API support. The key changes include:

1. Submodule Updates: Updates Git submodules for docs/notebooks and docs/faq to synchronize documentation with the latest autograd CM functionality
2. Code Reorganization: Moves simulation execution functions (_run_component_modeler and _compose_modeler_data_from_sim_map) from base.py to run.py to separate concerns and avoid circular imports
3. Autograd Integration: Adds support for autograd-enabled component modeler execution through the web API with new functions that handle simulation data mapping and autograd workflow
4. Test Updates: Refactors test imports from ComponentModeler to ModalComponentModelerData to align with the new architecture that separates modeler configuration from data/results classes
5. API Enhancements: Renames functions for better clarity (compose_simulation_data_index to compose_simulation_data_map) and improves error messages

The changes maintain backward compatibility while enabling component modelers to leverage the autograd web API execution path. This is part of a broader architectural shift to separate component modeler configuration from data handling, improving code organization and supporting advanced optimization workflows through autograd.

Important Files Changed

File Changes Summary

Filename	Score	Overview
docs/notebooks	5/5	Standard submodule update to synchronize notebooks with latest autograd CM changes
docs/faq	4/5	Submodule reference update that results in empty FAQ documentation directory
tidy3d/plugins/smatrix/component_modelers/base.py	4/5	Refactors code by moving simulation functions to run.py and updates type annotations
tests/test_plugins/smatrix/test_component_modeler_autograd.py	4/5	Updates test imports from ComponentModeler to ModalComponentModelerData for new architecture
tidy3d/plugins/smatrix/run.py	4/5	Adds autograd web API integration and new functions for component modeler execution

Confidence score: 4/5

• This PR is generally safe to merge with some areas requiring attention
• Score reflects solid refactoring with proper separation of concerns, but potential risks from circular imports and type safety changes
• Pay close attention to the base.py refactoring and ensure the empty FAQ submodule state is intentional

Sequence Diagram

sequenceDiagram
    participant User
    participant "Component Modeler" as CM
    participant "web.run" as WebRun
    participant "Autograd Engine" as AG
    participant "Batch Runner" as BR
    participant "Emulator/Solver" as Solver

    User->>CM: "build_modal_modeler(scale)"
    CM->>CM: "Create simulation with ports"
    User->>WebRun: "web.run(modeler, local_gradient=True)"
    WebRun->>AG: "_run_async with autograd support"
    AG->>CM: "Generate simulation dictionary"
    CM->>CM: "Create simulations for each port"
    AG->>BR: "Submit batch simulations"
    BR->>Solver: "Run simulations (forward + adjoint)"
    Solver->>BR: "Return simulation data"
    BR->>AG: "Compose simulation data map"
    AG->>CM: "_compose_modeler_data_from_sim_map"
    CM->>CM: "Create ComponentModelerData"
    WebRun->>User: "Return modeler_data with S-matrix"
    User->>User: "Extract S-matrix values for objective"
    User->>AG: "ag.grad(objective)(scale)"
    AG->>AG: "Compute gradients via backpropagation"
    AG->>User: "Return gradient value"

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[greptile-apps]

_{5 files reviewed, 2 comments}

_{Edit Code Review Bot Settings | Greptile}

[tylerflex]

Looks good 👍

[yaugenst-flex]

Minor nit otherwise looks good

[daquinteroflex]

Going to merge and test all runs from your branch