Validator: recognize .md doc ids, suppress ignored amendment rows by default, and add canonical-code metadata to many charters

[CAM-Initiative]

Motivation

• Improve cross-document § reference parsing to accept doc ids with optional .md extensions and common punctuation/spacing variants to reduce false negatives.
• Treat annex placeholder forms (e.g. Annex [x]) as manual-review cases rather than blocking or silently matching.
• Reduce noise in validator output by hiding amendment-register ignored rows by default while preserving the ability to show them with a flag.
• Publish source-authoritative "Canonical Code Status" and related metadata/ledger entries across multiple charter and schedule Markdown files and update the registry index versions.

Description

• Update validate_markdown_section_refs.py to use a DOC_ID_WITH_EXT_RE that accepts optional .md, broaden DOC_BEFORE_SECTION_RE/CROSS_DOC_AFTER_RE/PHRASE_DOC_SECTION_RE to handle punctuation/spacing, and ensure returned doc ids use the named capture doc_id.
• Add logic to classify annex-placeholder patterns as manual_review with a label Annex [x] when an explicit doc id plus an Annex placeholder is present.
• Change filter_display_findings and main to suppress IGNORED_STATUSES by default, add a --show-ignored CLI flag to restore display, and print a SUPPRESSED_IGNORED_ROWS summary when rows are hidden.
• Update tests in .github/scripts/tests/test_validate_markdown_section_refs.py to reflect the suppressed-ignored behaviour, and add tests covering CAM doc id variants and annex/placeholder cases.
• Add "Canonical Code Status" sections, renumbering and metadata updates, amendment-ledger entries, and minor provenance/metadata edits across many Governance/* Markdown files, and increment versions/pinned_sha/updated timestamps in constitution.index.json to reflect the content changes.

Testing

• Updated and ran the validator unit tests in .github/scripts/tests/test_validate_markdown_section_refs.py with pytest and confirmed the test suite for the validator changes passes.
• Exercised new cases for cross-document variants and annex-placeholder handling via added unit tests, which assert the validator returns pass_cross_document, manual_review variants, and that ignored amendment-register rows are suppressed by default; all assertions passed.
• Verified CLI behaviour: --show-ignored restores suppressed rows and the summary line SUPPRESSED_IGNORED_ROWS is emitted when suppression occurs during test runs.

---

Codex Task