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-audit/README.md

@@ -1,10 +1,27 @@
 # agent-audit
 
-Audits a Claude Code and Copilot agent definition file pair for correctness and quality.
+Audits an agent definition for correctness and quality — a single vendor-neutral file at
+plugin/APM scope, or a Claude Code and Copilot file pair at project/user scope.
 
 ## What it does
 
-Accepts either file in a CC `.md` / Copilot `.agent.md` pair, derives the counterpart automatically, and validates both. Runs structural checks via `validate.sh` (required fields, kebab-case name, no placeholders, no CC-only fields in the Copilot file, silently-ignored fields at plugin scope), provenance chain validation via `validate-provenance.sh` (checks `source_keys` against `sources.md` at the plugin root), then qualitative checks on description phrasing and system prompt quality. Step 1 also runs a Vale-based prose sub-check via `vale-wrap.sh` against both files of the pair, using the `Kyberforge` style (both files) and `KyberforgeCopilot` style (Copilot file only) — every alert is a `FAIL`, cited by rule ID — falling back to Step 2 judgment when the `vale` binary is unavailable or reports `0 files` scanned. Produces a compact findings report in the same format as `skill-audit`.
+At **plugin/APM scope**, accepts the single `.apm/agents/<name>.agent.md` file — there is no
+counterpart. Structural checks via `validate.sh` hard-`FAIL` any frontmatter field outside the
+vendor-neutral allowlist (`name`, `description`, `model` — see ADR-0016), since `apm compile`
+copies frontmatter verbatim to both harnesses and an unsafe field can't be silently dropped for
+just one of them.
+
+At **project/user scope**, accepts either file in a CC `.md` / Copilot `.agent.md` pair, derives
+the counterpart automatically, and validates both. Runs structural checks via `validate.sh`
+(required fields, kebab-case name, no placeholders, no CC-only fields in the Copilot file, no
+Copilot-only fields in the CC file), provenance chain validation via `validate-provenance.sh`
+(checks `source_keys` against `sources.md` at the plugin root — plugin/APM scope only), then
+qualitative checks on description phrasing and system prompt quality. Step 1 also runs a
+Vale-based prose sub-check via `vale-wrap.sh` against both files of the pair, using the
+`Kyberforge` style (both files) and `KyberforgeCopilot` style (Copilot file only) — every alert
+is a `FAIL`, cited by rule ID — falling back to Step 2 judgment when the `vale` binary is
+unavailable or reports `0 files` scanned. Produces a compact findings report in the same format
+as `skill-audit`.
 
 ## Usage
 

plugins/kyberforge/skills/agent-audit/scripts/validate.sh

@@ -185,6 +185,17 @@ def check_apm_agent_file(fpath, allowlist, stem):
         fail(f"no valid YAML frontmatter (---...---) — {local_fname}")
         return
 
+    # The apm-agent.md template embeds its authoring guidance as HTML
+    # comments inside the frontmatter block (so they render invisible in a
+    # Markdown preview but stay visible in the raw file). get_frontmatter_keys
+    # silently ignores any line that isn't a `key:` match, so a comment left
+    # behind at ship time would otherwise pass unnoticed — yet apm compile
+    # copies this frontmatter verbatim to both harnesses, and `<!-- -->` is
+    # not valid YAML, so yaml.safe_load breaks on both downstream (ADR-0016).
+    if re.search(r'<!--|-->', fm):
+        fail(f"frontmatter still contains template HTML comments (<!-- ... -->) "
+             f"— delete them before shipping — {local_fname}")
+
     # Allowlist: only name/description/model may appear — no tools, no
     # Claude-only or Copilot-only fields. apm compile verbatim-copies
     # frontmatter to every target, so anything else is unsafe on at least

plugins/kyberforge/skills/agent-audit/tests/validate.bats

@@ -92,6 +92,78 @@ EOF
     refute_output --partial "FAIL"
 }
 
+# ---------------------------------------------------------------------------
+# Failing cases — project/user scope: CC/Copilot pair checks
+# ---------------------------------------------------------------------------
+
+@test "fails when a CC-only field ('maxTurns') is present in a project-scope Copilot file" {
+    local root="$TMPDIR/project"
+    mkdir -p "$root/.git" "$root/.claude/agents" "$root/.github/agents"
+    cat > "$root/.claude/agents/my-agent.md" <<EOF
+---
+name: my-agent
+description: A valid agent description.
+---
+
+You are a test agent. When invoked, do the thing.
+EOF
+    cat > "$root/.github/agents/my-agent.agent.md" <<EOF
+---
+name: my-agent
+description: A valid agent description.
+maxTurns: 10
+---
+
+You are a test agent. When invoked, do the thing.
+EOF
+    run bash "$SCRIPT" "$root/.claude/agents/my-agent.md"
+    assert_failure
+    assert_output --partial "CC-only field"
+    assert_output --partial "maxTurns"
+}
+
+@test "fails when a Copilot-only field ('target') is present in a project-scope CC file" {
+    local root="$TMPDIR/project"
+    mkdir -p "$root/.git" "$root/.claude/agents" "$root/.github/agents"
+    cat > "$root/.claude/agents/my-agent.md" <<EOF
+---
+name: my-agent
+description: A valid agent description.
+target: cli
+---
+
+You are a test agent. When invoked, do the thing.
+EOF
+    cat > "$root/.github/agents/my-agent.agent.md" <<EOF
+---
+name: my-agent
+description: A valid agent description.
+---
+
+You are a test agent. When invoked, do the thing.
+EOF
+    run bash "$SCRIPT" "$root/.claude/agents/my-agent.md"
+    assert_failure
+    assert_output --partial "Copilot-only field"
+    assert_output --partial "target"
+}
+
+@test "fails when the Copilot counterpart is missing at project scope" {
+    local root="$TMPDIR/project"
+    mkdir -p "$root/.git" "$root/.claude/agents"
+    cat > "$root/.claude/agents/my-agent.md" <<EOF
+---
+name: my-agent
+description: A valid agent description.
+---
+
+You are a test agent. When invoked, do the thing.
+EOF
+    run bash "$SCRIPT" "$root/.claude/agents/my-agent.md"
+    assert_failure
+    assert_output --partial "counterpart file not found"
+}
+
 @test "--help exits 0 and shows Usage:" {
     run bash "$SCRIPT" --help
     assert_success
@@ -243,6 +315,29 @@ EOF
     assert_failure
 }
 
+@test "fails when a template HTML comment is left in plugin/APM-scope frontmatter" {
+    local root="$TMPDIR/pkg"
+    mkdir -p "$root/.apm/agents"
+    cat > "$root/apm.yml" <<EOF
+name: test-package
+version: 0.1.0
+type: skill
+EOF
+    cat > "$root/.apm/agents/my-agent.agent.md" <<EOF
+---
+name: my-agent
+description: A valid agent description.
+<!-- model: sonnet
+     Optional. Omit to inherit the runtime default. -->
+---
+
+You are a test agent. When invoked, do the thing.
+EOF
+    run bash "$SCRIPT" "$root/.apm/agents/my-agent.agent.md"
+    assert_failure
+    assert_output --partial "template HTML comments"
+}
+
 @test "fails when body contains unfilled FILL IN: placeholder in a plugin/APM-scope agent file" {
     local root="$TMPDIR/pkg"
     mkdir -p "$root/.apm/agents"

plugins/kyberforge/skills/agent-author/scripts/new-agent.sh

@@ -84,20 +84,23 @@ fi
 ROOT="$(cd "$ROOT" && pwd)"
 
 # True if apm_yml's top-level `type:` line names one of the four APM package
-# types (instructions/skill/hybrid/prompts) — tolerating an optional matching
-# quote around the value and requiring the value end there, so a malformed
-# value like `prompts-only` doesn't false-match on the `prompts` prefix.
+# types (instructions/skill/hybrid/prompts) — mirrors validate.sh's
+# APM_TYPE_RE: an optional quote around the value must be closed by the
+# *same* quote character (a mismatched or unterminated quote is rejected,
+# not silently stripped), and the value must be followed by whitespace or
+# end-of-line so `prompts-only` doesn't false-match on the `prompts` prefix.
+# `|| [[ -n "$line" ]]` in the read condition also processes a final line
+# that lacks a trailing newline, which `read` alone would otherwise skip.
 is_apm_package_manifest() {
-  local apm_yml="$1" line value
-  while IFS= read -r line; do
-    [[ "$line" =~ ^type:[[:space:]]*(.*)$ ]] || continue
-    value="${BASH_REMATCH[1]}"
-    value="${value%%[[:space:]]*}"
-    value="${value#\"}"; value="${value%\"}"
-    value="${value#\'}"; value="${value%\'}"
-    case "$value" in
-      instructions|skill|hybrid|prompts) return 0 ;;
-    esac
+  local apm_yml="$1" line
+  while IFS= read -r line || [[ -n "$line" ]]; do
+    if [[ "$line" =~ ^type:[[:space:]]*(instructions|skill|hybrid|prompts)([[:space:]]|$) ]]; then
+      return 0
+    fi
+    if [[ "$line" =~ ^type:[[:space:]]*([\"\'])(instructions|skill|hybrid|prompts)([\"\'])([[:space:]]|$) ]] \
+       && [[ "${BASH_REMATCH[1]}" == "${BASH_REMATCH[3]}" ]]; then
+      return 0
+    fi
   done < "$apm_yml"
   return 1
 }
@@ -110,44 +113,53 @@ is_apm_package_manifest() {
 #     (plugin/APM scope) — stop and return it.
 #   - an apm.yml with no `type:` field is a marketplace-only manifest — skip
 #     it, keep walking up.
-#   - reaching $HOME marks the user-scope boundary — stop, even if $HOME is
-#     itself a .git-tracked dotfiles directory (checked before the .git test
-#     below, so a dotfiles repo at $HOME can't shadow user scope).
+#   - user scope is checked directly at $HOME, no walk-up (see usage text
+#     above): ROOT itself being $HOME resolves to user scope, even if $HOME
+#     is itself a .git-tracked dotfiles directory (checked before the .git
+#     test below, so a dotfiles repo at $HOME can't shadow user scope).
+#     Walking *up into* $HOME from a nested directory with no apm.yml/.git
+#     of its own does NOT promote to user scope — it resolves to project
+#     scope instead, same as any other unmatched boundary, so a stray
+#     directory under $HOME can't be silently redirected into the shared
+#     global ~/.claude or ~/.copilot agent directories.
 #   - a .git file or directory marks the project-scope boundary (a worktree's
 #     .git is a file, not a directory) — stop.
-#   - filesystem root reached with neither found — boundary-reached.
+#   - filesystem root reached with neither found — project scope, same as
+#     any other unmatched boundary.
 find_package_root() {
-  local current="$1"
+  local root="$1" current="$1"
   while true; do
     if [[ -f "$current/apm.yml" ]] && is_apm_package_manifest "$current/apm.yml"; then
-      echo "plugin"
-      echo "$current"
+      echo "plugin $current"
       return
     fi
     if [[ "$current" == "$HOME" ]]; then
-      echo "user"
-      echo "$current"
+      if [[ "$current" == "$root" ]]; then
+        echo "user $current"
+        return
+      fi
+      echo "project $current"
       return
     fi
     if [[ -e "$current/.git" ]]; then
-      echo "project"
-      echo "$current"
+      echo "project $current"
       return
     fi
     local parent
     parent="$(dirname "$current")"
     if [[ "$parent" == "$current" ]]; then
-      echo "boundary-reached"
-      echo "$current"
+      echo "project $current"
       return
     fi
     current="$parent"
   done
 }
 
+# `read` consumes a single line, so kind and path are emitted on one
+# space-separated line rather than two `echo`s — kind first (never contains
+# spaces), path last (absorbs any spaces in the path safely).
 WALK_RESULT="$(find_package_root "$ROOT")"
-WALK_KIND="$(echo "$WALK_RESULT" | sed -n '1p')"
-WALK_ROOT="$(echo "$WALK_RESULT" | sed -n '2p')"
+read -r WALK_KIND WALK_ROOT <<< "$WALK_RESULT"
 
 PACKAGE_ROOT=""
 case "$WALK_KIND" in
@@ -161,11 +173,6 @@ case "$WALK_KIND" in
   project)
     SCOPE="project"
     ;;
-  boundary-reached)
-    # Default fallback, same as the pre-walk-up script: no plugin/APM
-    # marker, no $HOME boundary, and no .git means project scope.
-    SCOPE="project"
-    ;;
 esac
 
 # Determine file destinations

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
 # ---------------------------------------------------------------------------

plugins/kyberforge/skills/skill-author/scripts/new-skill.sh

@@ -82,21 +82,24 @@ if [[ ! -d "$TARGET_INPUT" ]]; then
 fi
 
 # True if apm_yml's top-level `type:` line names one of the four APM package
-# types (instructions/skill/hybrid/prompts) — tolerating an optional matching
-# quote around the value and requiring the value end there, so a malformed
-# value like `prompts-only` doesn't false-match on the `prompts` prefix.
+# types (instructions/skill/hybrid/prompts) — mirrors validate.sh's
+# APM_TYPE_RE: an optional quote around the value must be closed by the
+# *same* quote character (a mismatched or unterminated quote is rejected,
+# not silently stripped), and the value must be followed by whitespace or
+# end-of-line so `prompts-only` doesn't false-match on the `prompts` prefix.
+# `|| [[ -n "$line" ]]` in the read condition also processes a final line
+# that lacks a trailing newline, which `read` alone would otherwise skip.
 # Identical to agent-author's new-agent.sh copy of this helper.
 is_apm_package_manifest() {
-  local apm_yml="$1" line value
-  while IFS= read -r line; do
-    [[ "$line" =~ ^type:[[:space:]]*(.*)$ ]] || continue
-    value="${BASH_REMATCH[1]}"
-    value="${value%%[[:space:]]*}"
-    value="${value#\"}"; value="${value%\"}"
-    value="${value#\'}"; value="${value%\'}"
-    case "$value" in
-      instructions|skill|hybrid|prompts) return 0 ;;
-    esac
+  local apm_yml="$1" line
+  while IFS= read -r line || [[ -n "$line" ]]; do
+    if [[ "$line" =~ ^type:[[:space:]]*(instructions|skill|hybrid|prompts)([[:space:]]|$) ]]; then
+      return 0
+    fi
+    if [[ "$line" =~ ^type:[[:space:]]*([\"\'])(instructions|skill|hybrid|prompts)([\"\'])([[:space:]]|$) ]] \
+       && [[ "${BASH_REMATCH[1]}" == "${BASH_REMATCH[3]}" ]]; then
+      return 0
+    fi
   done < "$apm_yml"
   return 1
 }
@@ -105,7 +108,7 @@ is_apm_package_manifest() {
 # Walk up from <path> looking for a type-bearing apm.yml (package mode) or a
 # .git boundary / filesystem root (standalone mode). An apm.yml with no
 # top-level 'type:' field is a marketplace-only manifest — skip it and keep
-# walking up. Prints two lines: the resolved root, then the mode.
+# walking up. Prints one space-separated line: mode, then the resolved root.
 # ---------------------------------------------------------------------------
 find_package_root() {
   local current
@@ -113,8 +116,7 @@ find_package_root() {
   while true; do
     if [[ -f "$current/apm.yml" ]]; then
       if is_apm_package_manifest "$current/apm.yml"; then
-        echo "$current"
-        echo "package"
+        echo "package $current"
         return 0
       fi
       # apm.yml exists but has no type: field — marketplace-only manifest.
@@ -123,15 +125,13 @@ find_package_root() {
     # .git is a directory in a normal checkout but a file (`gitdir: ...`) in
     # a git worktree — -e covers both.
     if [[ -e "$current/.git" ]]; then
-      echo "$current"
-      echo "no-package"
+      echo "no-package $current"
       return 0
     fi
     local parent
     parent="$(dirname "$current")"
     if [[ "$parent" == "$current" ]]; then
-      echo "$current"
-      echo "no-package"
+      echo "no-package $current"
       return 0
     fi
     current="$parent"
@@ -139,10 +139,12 @@ find_package_root() {
 }
 
 # `mapfile`/`readarray` are bash 4.0+ builtins with no fallback on macOS's
-# stock /bin/bash 3.2 — read the two output lines individually instead.
+# stock /bin/bash 3.2 — read the single space-separated output line with a
+# plain `read` instead (bash 3.2-safe). `read` consumes only one line, so
+# mode and path must be on the same line: MODE first (never contains
+# whitespace), PKG_ROOT last (safely absorbs a path containing spaces).
 WALK_OUTPUT="$(find_package_root "$TARGET_INPUT")"
-PKG_ROOT="$(echo "$WALK_OUTPUT" | sed -n '1p')"
-MODE="$(echo "$WALK_OUTPUT" | sed -n '2p')"
+read -r MODE PKG_ROOT <<< "$WALK_OUTPUT"
 
 if [[ "$MODE" == "package" ]]; then
   TARGET="$PKG_ROOT/.apm/skills/$SKILL_NAME"

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"
+}