chore(#1671): widen the when= grammar and key the section manifest per workflow — Phase 6.1 (#3013)

* chore(#2992): widen the when= grammar and key the section manifest per workflow

Epic #1671 Phase 6.1. Two blockers stopped the fragment model reaching any
file beyond execute-phase.md: the when= vocabulary was frozen at 4 atoms
(3 execute-phase-specific), and the section manifest was single-workflow by
construction with 'execute-phase' hardcoded into buildSectionManifestField.

- widen WHEN_VOCABULARY 4 -> 14 via a coordinated ADR-1671 amendment; the
  grammar stays CLOSED (one atom, no operators, negation or nesting) and
  WHEN_PREDICATES stays a hand-written literal map, never deriving a
  predicate from its atom string
- InvocationFacts gains flags: ReadonlySet<string> plus three computed state
  booleans; add the missing reverse vocabulary/predicate parity guard
- key the manifest artifact per workflow; a stale flat {sections:[...]}
  artifact now fails shape validation instead of being misattributed
- wire the field into six init entry points and parse the flags each needs

An atom ships only with both a real consuming section and a fact the init
seam actually computes. Six surveyed atoms are withheld because their
workflows have no dedicated init entry point; an atom without a computed
fact evaluates false forever and silently disables its own section.

Fixes a defect found while wiring: parseNamedArgs always materializes a
boolean flag key, so folding its false into the absent sentinel is required
or every flag reads as present and gating is silently always-on.

Also resolves ADR-1671:194 by measurement: --mvp stays unmarkable, because
its interleaved sites are always-run flag resolution and a ~340 byte block
that already delegates lazily.

Refs #2992

* fix(#2992): treat any falsy option value as an absent flag and reject unsafe manifest read paths

Findings from two orthogonal reviews (Claude /code-review + an isolated
adversarial pass); both independently reproduced the first one.

- MAJOR: the flags-builder treated only `undefined` as absent, but
  parseNamedArgs yields `null` for an absent value-flag and `false` for an
  absent boolean-flag, so `--granularity` read as present on every
  plan-phase invocation. Fixed at the root: a flag is present iff its
  option value is truthy. The six per-handler `|| undefined` folds are now
  redundant and removed, which also closes the duplicate-translation and
  missed-onboard-handler findings.
- MAJOR: state:needs-codebase-map had zero coverage. Added unit, property
  and real-CLI integration tests.
- MINOR: reject absolute, UNC/drive and `..`-traversing `read` paths in the
  manifest, degrading the whole load to null like every other shape
  violation. Verified: `/etc/passwd` previously reached section_manifest.read.
- MINOR: corrected a stale "4 to 20" doc comment; the vocabulary is 14.

Refs #2992

* test(#2992): update the generator suite for the per-workflow manifest shape

The remote matrix went red with 5 unique failures, identical on
linux-node22 and linux-node24, all in tests/gen-section-manifest.test.cjs.
Re-keying the artifact to {workflows:{...}} left this suite asserting the
old flat {sections:[...]} shape; nothing else in the tree still does.

- three tests read manifest.sections.length, now undefined; retargeted at
  workflows.<name> with their original intent preserved (a fenced or
  loop-host marker still asserts NO section is produced, not merely a
  changed count)
- the stale-manifest test wrote its fixture in the OLD shape, so it tripped
  shape validation and stopped exercising staleness at all. Its fixture is
  now valid-but-mismatched so FAIL_STALE is genuinely reached again.
- added the coverage that exposed: a pre-6.1 flat artifact must report
  FAIL_MANIFEST_MALFORMED_SHAPE. That is the real upgrade path for an
  installed tree and nothing covered it.

Refs #2992

* chore(#2992): backfill changeset pr number to 3013

---------

Co-authored-by: sim <sim@local>

.changeset/merry-bears-purr.md

@@ -0,0 +1,5 @@
+---
+type: Changed
+pr: 3013
+---
+**Documented the widened `when=` vocabulary and the per-workflow section manifest.** `docs/reference/workflow-fragments.md` now lists all 14 closed `when=` atoms, the two admission gates a new atom must clear, the manifest artifact's per-workflow `{workflows:{<name>:[...]}}` shape (absent key = degraded, empty array = computed-empty), and that boolean-flag membership in `InvocationFacts.flags` is token-presence, not value-truthiness. Also added the missing `--reset-phase-numbers` flag to `/gsd-new-milestone`'s argument-hint. (#2992)