[codex] Reorganize repository layout

[FlorianPfaff]

Summary

• Move the package from pyrecest/ to src/pyrecest/.
• Move tests from pyrecest/tests/ to top-level tests/ and update the affected test imports.
• Move update_init_helper.py into tools/, add placeholder example directories, and update CI/lint/devcontainer paths for the src layout.

Validation

• Verified the generated branch tree has no root pyrecest/ directory, no src/pyrecest/tests/, and includes src/pyrecest/, tests/, tools/, and examples/.
• Did not run the full test suite locally; this branch was created through GitHub tree operations rather than a local checkout.

[github-actions]

✅MegaLinter analysis: Success

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ COPYPASTE	jscpd	yes		no	no	12.49s
✅ JSON	prettier	2	0	0	0	0.41s
✅ JSON	v8r	2		0	0	2.28s
✅ MARKDOWN	markdownlint	2	0	0	0	0.66s
✅ MARKDOWN	markdown-table-formatter	2	0	0	0	0.29s
✅ PYTHON	bandit	372		0	0	5.49s
✅ PYTHON	black	372	20	0	0	9.29s
✅ PYTHON	flake8	372		0	0	3.09s
✅ PYTHON	isort	372	22	0	0	0.73s
✅ PYTHON	mypy	372		0	0	4.94s
✅ PYTHON	pylint	372		0	0	109.91s
✅ PYTHON	ruff	372	22	0	0	0.08s
✅ REPOSITORY	checkov	yes		no	no	23.07s
✅ REPOSITORY	gitleaks	yes		no	no	6.88s
✅ REPOSITORY	git_diff	yes		no	no	0.11s
✅ REPOSITORY	secretlint	yes		no	no	6.45s
✅ REPOSITORY	syft	yes		no	no	4.21s
✅ REPOSITORY	trivy-sbom	yes		no	no	2.44s
✅ REPOSITORY	trufflehog	yes		no	no	19.41s
✅ YAML	prettier	4	0	0	0	0.49s
✅ YAML	v8r	4		0	0	4.65s
✅ YAML	yamllint	4		0	0	0.42s

See detailed reports in MegaLinter artifacts

Your project could benefit from a custom flavor, which would allow you to run only the linters you need, and thus improve runtime performances. (Skip this info by defining FLAVOR_SUGGESTIONS: false)

• Documentation: Custom Flavors
• Command: npx mega-linter-runner@9.4.0 --custom-flavor-setup --custom-flavor-linters PYTHON_PYLINT,PYTHON_BLACK,PYTHON_FLAKE8,PYTHON_ISORT,PYTHON_BANDIT,PYTHON_MYPY,PYTHON_RUFF,COPYPASTE_JSCPD,JSON_V8R,JSON_PRETTIER,MARKDOWN_MARKDOWNLINT,MARKDOWN_MARKDOWN_TABLE_FORMATTER,REPOSITORY_CHECKOV,REPOSITORY_GIT_DIFF,REPOSITORY_GITLEAKS,REPOSITORY_SECRETLINT,REPOSITORY_SYFT,REPOSITORY_TRIVY_SBOM,REPOSITORY_TRUFFLEHOG,YAML_PRETTIER,YAML_YAMLLINT,YAML_V8R

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[github-actions]

Test Results

    12 files     12 suites   4h 38m 25s ⏱️
 1 042 tests 1 042 ✅     0 💤 0 ❌
12 788 runs  9 876 ✅ 2 912 💤 0 ❌

Results for commit 6ae69a9.

♻️ This comment has been updated with latest results.