fix(gates): close the review findings in the gates and their docs

Two reproduced bugs in check-skill-version-bump:

- The origin/main-tip check fired even when the pushed skill was
  byte-identical to main's tip, so a cherry-pick or backport failed a
  push that ships nothing. The merge-base intersection ea119d8 added
  covers that only when some base carries the content, which a
  criss-cross history gives and a linear one does not. A new
  same_subtree compares tree object ids, so the exemption holds
  whatever route the history took.
- The failure line reported "baseline: none" when the skill was absent
  at every merge-base but present at the tip, and the Fix: line then
  named no version. The author writes the natural 1.0.0 and gets a
  second blocked push. It now falls back to the tip's version.

ADR-0022 is not amended: the documented behaviour does not change, and
ea119d8 set the precedent by fixing the same failure class script-only.

1614bce verified that executables.allow grants are version-blind and
corrected ADR-0019, gates.md and apm.yml, but missed the gate script's
own header and its operator-facing FAIL message, which still told the
reader deployment was silently broken, and gates.md's hook summary,
which still called it a silent-failure guard. All three now match.

Also: README's offline guarantee carries the populated-apm_modules
condition gates.md and AGENTS.md already state; the scripts/ layout row
drops "sync" for the three deleted sync scripts; the check-rtk-prefix
README rationale names the 12 subdirectory READMEs that survive rather
than the skill-root ones this branch deleted; gates.md re-cites its
three head -1 sites by enclosing function per its own :238 rule; and
deploy-manifest drops a pointer to a provider-manifest.sh that has
never existed on main.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01NwD8Egs5r4ndqeFLmhusX2

README.md

@@ -12,7 +12,7 @@ Content ships as six installable plugins, each an apm (Agent Package Manager) pa
 | `providers/claude-code/` | Claude Code adapter, deployed to `~/.claude/` via `scripts/install.sh` |
 | `core/` | Provider-agnostic always-on content — `core/AGENTS.md` and `core/instructions/` |
 | `docs/` | Specs (`docs/spec/`), architectural decisions (`docs/adr/`), governance, research, and notes |
-| `scripts/` | Install, sync, and check scripts used by the git hooks |
+| `scripts/` | Install and check scripts used by the git hooks |
 | `tests/` | `run-tests.sh`, `run-bats.sh`, the `test-*.sh` suites, and the bats submodules |
 
 The six plugins:
@@ -86,7 +86,7 @@ pre-commit run --hook-stage pre-push --all-files
 
 See [`docs/spec/gates.md`](docs/spec/gates.md) for what each hook enforces and why.
 
-**Offline?** No pre-push hook needs the network: root `apm.yml`'s marketplace has no remote package entries (the last one, `mattpocock-skills`, was removed), so `apm-pack-check-clean` resolves everything from local sources. All pre-push hooks pass offline.
+**Offline?** No pre-push hook needs the network **once `apm install` has populated `apm_modules/`**. Root `apm.yml`'s marketplace has no remote package entries (the last one, `mattpocock-skills`, was removed), so `apm-pack-check-clean` resolves everything from local sources, and `apm-audit-ci`'s install-replay is cache-only against a populated install. On a **fresh clone** there is no cache: `apm-audit-ci`'s `deployed-files-present` fails outright, and its `drift` and `config-consistency` checks clone from the holocron remote. The offline guarantee is a property of a populated `apm_modules/`, not of the hook set — run `apm install` once on a new checkout and it holds from then on.
 
 ## Editing plugin content