[glrs]

This PR focuses on post-merge corrections and clarifications for the package consolidation work, along with several workflow and documentation improvements. The most significant changes address Python package discovery and structure, clarify documentation around known limitations and references to tech debt, and update CI workflows to use the latest GH Actions.

Python packaging and structure:

• Changed package discovery in pyproject.toml to disable namespace packages by setting namespaces = false, ensuring only directories with an __init__.py are included as packages.
• Added a missing __init__.py to yggdrasil/flow/utils/ to ensure it is recognized as a package.
• Added a test (tests/test_package_layout.py) to verify that every source directory containing Python modules has an __init__.py, preventing accidental omission from distributions.

Documentation and tech debt clarifications:

• Updated documentation (including CLAUDE.md, README.md, and overview.md) to remove references to the number of tests and to clarify that known gaps should be described directly, not just cited via a tech-debt ledger, since the ledger is untracked. [1] [2] [3] [4]
• Revised plan and PRD documentation to add a "Post-merge corrections" section, detailing changes to package discovery, namespace settings, and docstring conventions regarding known gaps and tech debt. [1] [2] [3] [4] [5] [6]

Docstring and code comments updates:

• Updated docstrings in several core classes (OpsWriter, PlanBuilder, YggdrasilCore, etc.) to explain limitations directly instead of referencing the untracked tech-debt ledger. [1] [2] [3]

CI/CD workflow updates:

• Updated GitHub Actions in all workflow files (docs.yml, lint.yml, security.yml, tests.yml) to use the latest major versions of actions/checkout, actions/setup-python, and related actions for improved security and support. [1] [2] [3] [4] [5] [6] [7] [8]

These changes ensure the package structure is robust and discoverable, CI is up-to-date, and documentation accurately reflects current practices and known limitations.

References:
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24]