Integrate SQLite, CRT/IAT workflows, and NEcost examples

[JiaZhou-PU]

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Merge Request Description

Summary

This PR integrates the recent ACCERT workflow updates into development.

Added

• SQLite-backed ACCERT database setup and procedures.
• CRT workflow package, examples, sampling utilities, and visualization support.
• IAT API/data updates and ACCERT-to-IAT/CRT bridge utilities.
• Combined CRT/IAT GUI workflow and tutorial examples.
• Expanded NEcost tutorial cases and report-check examples.

Changed

• Reorganized Workbench templates into ACCERT, NEcost, and common template namespaces.
• Renamed CRF workflow references to CRT.
• Updated documentation for install, examples, CRT, IAT, GUI workflow, and NEcost usage.
• Refreshed integration gold outputs and regression coverage.

Removed

• Legacy MySQL test/workflow pieces.
• Old generated documentation and obsolete template locations.

Testing

pytest                                 34s  accert 03:58:42 PM

================================================== test session starts ===================================================
platform darwin -- Python 3.12.13, pytest-9.1.1, pluggy-1.6.0
rootdir: /Users/jia.zhou/projects/ACCERT
configfile: pyproject.toml
plugins: anyio-4.9.0
collected 77 items

test_crt_api.py ......                                                                                             [  7%]
test_gui_workflow.py ..                                                                                            [ 10%]
test_iat_api.py ................                                                                                   [ 31%]
test_integration.py ......                                                                                         [ 38%]
test_main.py ..............................                                                                        [ 77%]
test_monte_carlo_sampler.py ...                                                                                    [ 81%]
test_necost_workflow.py ..........                                                                                 [ 94%]
test_sqlite.py ...                                                                                                 [ 98%]
test_util.py .                                                                                                     [100%]

Notes

This branch is intended to merge into accert-dev/ACCERT:development.

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For Change Request Review

• 1. Is the merge request reference an issue? If the issue is closed, the issue close checklist shall be done.
• 2. Is the merge request reference a task? If the task is fulfilled, the task close checklist shall be done.
• 3. If any changes to the database, there must be an accompanying change to the all the linked tables.

[JiaZhou-PU]

@nstauff Ready for review

[nstauff]

This looks great and will be a major release for ACCERT. In the future, I recommend trying to break down the different MR into smaller changes to avoid such large review.

[JiaZhou-PU]

Thanks! I will address the comments today

[JiaZhou-PU]

Resolved most comments

[JiaZhou-PU]

@nstauff, except for the NECOST request, all comments are addressed.