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/vendor/update.go

@@ -226,7 +226,7 @@ func availableSince(old map[string]map[string]bool, items []discovery.Item, sele
 	inSelection := idSet(selected)
 	out := map[string][]string{}
 	for _, it := range items {
-		if old[it.Type][it.UpstreamID] || inSelection[it.Type][it.UpstreamID] {
+		if it.Skipped || old[it.Type][it.UpstreamID] || inSelection[it.Type][it.UpstreamID] {
 			continue
 		}
 		out[it.Type] = append(out[it.Type], it.UpstreamID)