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/agent-author/tests/new-agent.bats

@@ -130,6 +130,29 @@ teardown() {
     assert [ -f "$ROOT/.apm/agents/my-agent.agent.md" ]
 }
 
+@test "plugin/APM scope: matched-quote type value ('skill') is recognized" {
+    printf 'name: my-package\ntype: "skill"\n' > "$ROOT/apm.yml"
+    run bash "$SCRIPT" my-agent "$ROOT"
+    assert_success
+    assert [ -f "$ROOT/.apm/agents/my-agent.agent.md" ]
+}
+
+@test "plugin/APM scope: mismatched-quote type value is rejected, falls through to project scope" {
+    mkdir -p "$ROOT/.git"
+    printf "name: my-package\ntype: \"skill'\n" > "$ROOT/apm.yml"
+    run bash "$SCRIPT" my-agent "$ROOT"
+    assert_success
+    assert [ ! -f "$ROOT/.apm/agents/my-agent.agent.md" ]
+    assert [ -f "$ROOT/.claude/agents/my-agent.md" ]
+}
+
+@test "plugin/APM scope: type: line is recognized even without a trailing newline on the file" {
+    printf 'name: my-package\ntype: skill' > "$ROOT/apm.yml"
+    run bash "$SCRIPT" my-agent "$ROOT"
+    assert_success
+    assert [ -f "$ROOT/.apm/agents/my-agent.agent.md" ]
+}
+
 # ---------------------------------------------------------------------------
 # Old plugin.json marker is no longer recognized (full switch, no dual-mode)
 # ---------------------------------------------------------------------------
@@ -222,6 +245,18 @@ teardown() {
     rm -rf "$FAKE_HOME"
 }
 
+@test "user scope is checked directly at \$HOME, no walk-up: a marker-less subdir under \$HOME resolves to project scope, not user scope" {
+    FAKE_HOME="$(mktemp -d)"
+    mkdir -p "$FAKE_HOME/scratch/testdir"
+    run env HOME="$FAKE_HOME" bash "$SCRIPT" my-agent "$FAKE_HOME/scratch/testdir"
+    assert_success
+    assert [ -f "$FAKE_HOME/scratch/testdir/.claude/agents/my-agent.md" ]
+    assert [ -f "$FAKE_HOME/scratch/testdir/.github/agents/my-agent.agent.md" ]
+    refute [ -f "$FAKE_HOME/.claude/agents/my-agent.md" ]
+    refute [ -f "$FAKE_HOME/.copilot/agents/my-agent.agent.md" ]
+    rm -rf "$FAKE_HOME"
+}
+
 # ---------------------------------------------------------------------------
 # Name validation
 # ---------------------------------------------------------------------------