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

plugins/kyberforge/skills/skill-author/tests/new-skill.bats

@@ -184,3 +184,25 @@ EOF
     assert [ -d "$DEST/repo/sub/my-tool" ]
     assert [ ! -d "$DEST/repo/my-tool" ]
 }
+
+@test "package mode: matched-quote type value ('skill') is recognized" {
+    mkdir -p "$DEST/pkg"
+    printf 'name: my-pkg\ntype: "skill"\n' > "$DEST/pkg/apm.yml"
+    run bash "$SCRIPT" my-tool "$DEST/pkg"
+    assert_success
+    assert_output --partial "Mode: package"
+}
+
+@test "mismatched-quote type value is rejected, falls through to standalone mode" {
+    printf "name: my-pkg\ntype: \"skill'\n" > "$DEST/apm.yml"
+    run bash "$SCRIPT" my-tool "$DEST"
+    assert_success
+    assert_output --partial "Mode: standalone"
+}
+
+@test "type: line is recognized even without a trailing newline on apm.yml" {
+    printf 'name: my-pkg\ntype: skill' > "$DEST/apm.yml"
+    run bash "$SCRIPT" my-tool "$DEST"
+    assert_success
+    assert_output --partial "Mode: package"
+}