feat(discovery): frontmatter guard for flat agents/commands docs

A flat .md under agents/ or commands/ whose frontmatter contains none of
the definition keys (name, description, mode, agent, model,
argument-hint, temperature, permission) is documentation, not an item:
discovery marks it Skipped with a recorded warning — it never enters a
selection, inventory, availability listing or collision index, but the
warning lands in the lockfile and add/update/select reports like other
discovery warnings. Skills keep their folder+SKILL.md marker, MCP keeps
the .yaml marker. README gains the canonical layout table and the
migration note for folder-style agent repos.

Closes beads: agent-lib-2n7

internal/e2e/skip_docs_test.go

@@ -0,0 +1,86 @@
+package e2e
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func docFixture(h *harness, t *testing.T) {
+	t.Helper()
+	h.write(t, "skills/good-skill/SKILL.md", "---\nname: Good Skill\ndescription: works\n---\n# Good\n")
+	h.write(t, "agents/scout.md", "---\ndescription: a real agent\n---\nbody\n")
+	h.write(t, "agents/SCHEMA.md", "# Schema\npure documentation, no frontmatter\n")
+	h.write(t, "commands/review.md", "---\nargument-hint: [files]\n---\nbody\n")
+	h.write(t, "commands/README.md", "Documentation for the commands directory.\n")
+	h.commitUpstream(t, "fixture with documentation files")
+}
+
+func TestVendorAddSkipsDocMarkdownWithWarning(t *testing.T) {
+	h := newHarness(t)
+	docFixture(h, t)
+
+	out := h.mustRun(t, "vendor", "add", "superpowers", h.upstreamDir)
+	if !contains(out, "agents/SCHEMA.md: no agent frontmatter, skipped") {
+		t.Errorf("add report must warn about skipped SCHEMA.md:\n%s", out)
+	}
+	if !contains(out, "commands/README.md: no command frontmatter, skipped") {
+		t.Errorf("add report must warn about skipped README.md:\n%s", out)
+	}
+
+	lock := readFile(t, filepath.Join(h.workDir, "agent-lib.lock.json"))
+	if !contains(lock, "agents/SCHEMA.md: no agent frontmatter, skipped") {
+		t.Errorf("lockfile warnings must record the skip:\n%s", lock)
+	}
+	for _, dir := range []string{"agents", "commands"} {
+		entries, err := os.ReadDir(filepath.Join(h.workDir, "external", "superpowers", dir))
+		if err != nil {
+			t.Fatalf("external %s area must exist: %v", dir, err)
+		}
+		for _, e := range entries {
+			name := e.Name()
+			if (dir == "agents" && name == "SCHEMA.md") || (dir == "commands" && name == "README.md") {
+				t.Errorf("documentation file %s/%s must not be materialized", dir, name)
+			}
+		}
+	}
+	if !contains(out, "1 agents") || !contains(out, "1 commands") {
+		t.Errorf("counts must reflect real items only:\n%s", out)
+	}
+	h.mustRun(t, "validate")
+}
+
+func TestVendorAddIncludeErrorOmitsSkippedDocs(t *testing.T) {
+	h := newHarness(t)
+	docFixture(h, t)
+
+	out, err := h.run(t, "vendor", "add", "superpowers", h.upstreamDir, "--include", "typo")
+	if err == nil {
+		t.Fatalf("include with typo must fail:\n%s", out)
+	}
+	if contains(out, "SCHEMA") || contains(out, "README") {
+		t.Errorf("skipped documentation must not appear as available ids:\n%s", out)
+	}
+	for _, want := range []string{"scout", "review", "good-skill"} {
+		if !contains(out, want) {
+			t.Errorf("real ids must still be listed as available (missing %s):\n%s", want, out)
+		}
+	}
+}
+
+func TestVendorUpdateSelectKeepSkippingDocs(t *testing.T) {
+	h := newHarness(t)
+	docFixture(h, t)
+	h.mustRun(t, "vendor", "add", "superpowers", h.upstreamDir, "--include", "scout,review")
+
+	out := h.mustRun(t, "vendor", "select", "superpowers", "--add", "good-skill")
+	if contains(out, "SCHEMA") {
+		t.Errorf("select report must not surface skipped docs:\n%s", out)
+	}
+	lock := readFile(t, filepath.Join(h.workDir, "agent-lib.lock.json"))
+	if got := strings.Count(lock, "no agent frontmatter, skipped"); got != 1 {
+		t.Errorf("warning must stay recorded exactly once in the lockfile, got %d", got)
+	}
+	h.mustRun(t, "validate")
+}