fix(kyberforge): fix scope walk-up and manifest-parsing bugs from PR #93 review

A fresh /code-review of the APM-native authoring retarget (PR #93) found
several correctness bugs beyond the ones already fixed on this branch:

- new-agent.sh silently walked a marker-less subdirectory under $HOME up
  to user scope, contradicting its own usage text ("user scope is checked
  directly, no walk-up") and risking scaffolding into shared global
  ~/.claude or ~/.copilot directories instead of the intended local path.
- The hand-copied apm.yml type: manifest detector in new-agent.sh and
  new-skill.sh accepted mismatched quotes (e.g. `type: "skill'`) that
  validate.sh's regex correctly rejects, and silently dropped a final
  apm.yml line lacking a trailing newline — causing the scaffolder and
  validator to disagree on scope for identical input.
- Plugin-scope agent frontmatter could still contain the apm-agent.md
  template's HTML comments at ship time with no audit signal, yet
  apm compile copies frontmatter verbatim and <!-- --> breaks YAML
  parsing on both downstream harnesses.
- ADR-0016 asserted agent-audit already implements a SUGGESTION heuristic
  for tool-restriction-needing plugin-scope agents; it doesn't.
- agent-audit/README.md still described the old plugin-pair model this
  PR replaced with a single-file allowlist model.
- validate.sh's project/user-scope CC-only/Copilot-only field checks and
  counterpart-missing check lost their only test coverage when the old
  plugin-pair fixture was deleted.

Also replaces an echo-into-sed two-value parse (4 forks per call) with a
single space-separated echo + read in both scaffolders.

Regression tests added for every fix above, including one for a bug this
pass introduced and the test suite caught: an initial two-line
echo + `read` attempt silently dropped the second value, since `read`
consumes only one line regardless of embedded newlines.

Full suite: 158 bats tests, 39 shell-script tests, 12/12 summary
categories, 0 failures.

Refs: #89, #93

docs/adr/0016-apm-agent-primitive-drops-provider-specific-fields.md

@@ -40,11 +40,13 @@ Absent `tools:` means inherit-all-tools on both harnesses — the one value that
 on either target, unlike a present, harness-specific value that is guaranteed wrong on at least
 one of them.
 
-`agent-audit`, at plugin scope, flags — as a **SUGGESTION**, not a FAIL, since this is an
-upstream schema limitation rather than an authoring mistake — any agent whose description or
-body implies a need for tool restriction or a Claude-only behavior the frontmatter can no
-longer express. This gives visibility into the gap without pretending the schema can do
-something it can't.
+`agent-audit`, at plugin scope, is intended to flag — as a **SUGGESTION**, not a FAIL, since
+this is an upstream schema limitation rather than an authoring mistake — any agent whose
+description or body implies a need for tool restriction or a Claude-only behavior the
+frontmatter can no longer express. This would give visibility into the gap without pretending
+the schema can do something it can't. **Not yet implemented**: `check_apm_agent_file()` in
+`validate.sh` currently validates only the field allowlist, `name`, `description`, and
+body-emptiness/length — it has no heuristic for this case. Tracked as follow-up work.
 
 ### Scope boundary