[codex] Fix groundtruth object-array indexing

[FlorianPfaff]

Summary

• Read prior ground-truth states through the per-timestep object-array entry before indexing target rows.
• Reuse a has_inputs flag so inputs=None is treated the same as missing inputs.
• Use column-oriented controls (inputs[:, t - 1]) to match the existing (input_dim, n_timesteps - 1) assertion.
• Add regression tests for noisy transitions, noiseless transitions, and input-driven transitions over multiple targets.

Root cause

generate_groundtruth stores each timestep as an element in a one-dimensional object array. Some custom transition paths indexed it as if it were a dense multidimensional array, which raises before transition callbacks can run. The input-driven branch also read rows from inputs even though the function validates inputs as timestep columns.

Validation

• Inspected the branch diff through the GitHub connector.
• Not run locally: this Codex session has a read-only filesystem, so changes were applied via GitHub API rather than a local checkout.

[github-actions]

✅MegaLinter analysis: Success

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ COPYPASTE	jscpd	yes		no	no	15.14s
✅ JSON	prettier	2	0	0	0	0.45s
✅ JSON	v8r	2		0	0	2.73s
✅ MARKDOWN	markdownlint	2	0	0	0	0.64s
✅ MARKDOWN	markdown-table-formatter	2	0	0	0	0.2s
✅ PYTHON	bandit	394		0	0	5.48s
✅ PYTHON	black	394	6	0	0	7.98s
✅ PYTHON	flake8	394		0	0	2.98s
✅ PYTHON	isort	394	10	0	0	0.73s
✅ PYTHON	mypy	394		0	0	4.77s
✅ PYTHON	pylint	394		0	0	117.72s
✅ PYTHON	ruff	394	10	0	0	0.07s
✅ REPOSITORY	checkov	yes		no	no	21.66s
✅ REPOSITORY	gitleaks	yes		no	no	10.8s
✅ REPOSITORY	git_diff	yes		no	no	0.06s
✅ REPOSITORY	secretlint	yes		no	no	6.83s
✅ REPOSITORY	syft	yes		no	no	3.13s
✅ REPOSITORY	trivy-sbom	yes		no	no	2.41s
✅ REPOSITORY	trufflehog	yes		no	no	19.62s
✅ YAML	prettier	4	0	0	0	0.44s
✅ YAML	v8r	4		0	0	4.41s
✅ YAML	yamllint	4		0	0	0.43s

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[github-actions]

Test Results

    12 files  +    10      12 suites  +10   4h 28m 22s ⏱️ + 4h 8m 42s
 1 126 tests +     3   1 126 ✅ +    4      0 💤  -     1  0 ❌ ±0 
13 804 runs  +11 503  10 536 ✅ +8 838  3 268 💤 +2 665  0 ❌ ±0 

Results for commit d0d9a57. ± Comparison against base commit dc8dc2b.

♻️ This comment has been updated with latest results.