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Tom Boucher c5b83cb050 chore(#3560 ): delete two unreachable workflows, gate workflow reachability in lint (#3564 )

* chore(#3560): delete two unreachable workflows, gate reachability in lint

discovery-phase.md and plan-milestone-gaps.md shipped to all 19 runtime
install trees with no command, agent, or skill referencing them.
plan-milestone-gaps' command was deleted by #2790 and the workflow was
left behind; discovery-phase's own header claimed a caller in
plan-phase.md's mandatory_discovery step, and that step does not exist —
plan-phase.md contains zero occurrences of "discovery".

docs/INVENTORY.md asserted discovery-phase.md was an alternate entry for
/gsd-new-project. new-project.md never referenced it. The row and the
matching note sentence are removed across all five locales rather than
corrected.

Adds rule 6 to lint-command-contract: every shipped workflow must be
reachable from a loader, walking the transitive closure over the three
reference shapes this repo uses. The closure seeds ONLY from
commands/agents/skills, so a workflow that references only itself and a
pair that reference only each other are both correctly reported rather
than satisfying themselves; a visited set makes reference cycles
terminate. The measure is a mention in a LOADER — docs/ and install-tree
fixtures deliberately do not count, because scan.md proved a file can be
documented and shipped while entirely unreached.

Ships blocking, not report-only: #3561 is in this branch's base, so the
tree reports 0 unreachable from the start.

Closes #3560

* test(#3560): drive rule 6 end-to-end, sweep a stale allowlist, update ADR-0002

Review findings.

Rule 6 had no end-to-end coverage: the tests exercised the pure closure
with in-memory data, so the wiring — file collection, exit code,
diagnostic — was unproven, and #3560's acceptance list explicitly wants
a fixture showing the rule FAILS on a planted orphan. Adds an optional
--root to lint-command-contract (default behavior unchanged) and four
tests driving the real CLI through the process seam against a temp
fixture: clean=0, planted orphan=1, orphan referenced only from docs/=1,
orphan reachable transitively=0. The docs/ case is what pins the
Goodhart defense — a mention outside a loader must not confer
reachability.

Deletes two tests that were byte-identical to a third and could not
assert anything loader-specific, since the closure is source-agnostic by
design; that distinction lives in the lint script's file collection and
is now covered above.

Removes a stale ALLOWLIST entry for discovery-phase.md in
planner-language-regression — the exact sweep-miss class rule 6 exists
to catch, found in the PR that adds the rule.

ADR-0002 described five per-file frontmatter checks; rule 6 is a
repo-level reachability graph, so the Decision section now says so.

Refs #3560

* test(#3560): cut the bug-3298 test pin on the deleted plan-milestone-gaps workflow

The remote runner went red with four failures: tests/phase.test.cjs
asserted the plan-milestone-gaps workflow exists and checked its mkdir
patterns, so deleting the file broke the test that pinned it. This is the
fence the epic describes — the content-sync test IS what keeps an
unreachable file alive — and cutting the coupling is what makes the
deletion safe.

Removes only that arm. The bug-3298 block guards three workflows against
phase-dir prefix drift; the import and add-backlog arms and both shared
mkdir-pattern helpers are untouched.

Worth recording where the sweep failed: my reachability walk covered
commands, agents, skills, gsd-core and docs, and lint-removed-but-needed
covers .github/workflows, gsd-core, docs and package.json. Neither looks
at tests/, so a test-pinned deletion is invisible to both and surfaces
only on the remote runner. The how-to added by this PR names that gap
explicitly so the next deletion searches tests/ by hand.

Refs #3560

* docs(#3560): add a how-to for resolving unreachable-workflow findings

* chore(#3560): backfill changeset pr number to 3564

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