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/collide.go

@@ -39,6 +39,9 @@ func ownDeployed(workDir string) (deployedIndex, error) {
 	}
 	idx := deployedIndex{}
 	for _, it := range items {
+		if it.Skipped {
+			continue
+		}
 		idx.add(it.Type, it.UpstreamID, owner{source: "own", id: it.UpstreamID})
 	}
 	return idx, nil