Update cli.js

cli.js

@@ -3,6 +3,7 @@
 const { createMUE } = require('./mue');
 const { compileMUE } = require('./muc');
 const { registerMU } = require('./mur');
+const { registerSpecies } = require('./sei');
 const { processSignal } = require('./engine');
 const { actuatorEnvelope } = require('./actuator');
 
@@ -10,7 +11,7 @@ const input = process.argv[2];
 
 if (!input) {
   console.error('Error: No input signal provided.');
-  console.error('Usage: node cli.js \"your-signal\"');
+  console.error('Usage: node cli.js "your-signal"');
   process.exit(1);
 }
 
@@ -26,20 +27,24 @@ const mue = createMUE(input);
 // Step 2 — MUC
 const mu = compileMUE(mue);
 
-// Step 3 — Register MU
+// Step 3 — Register MU in MUR
 const registry = registerMU(mu);
 
-// Step 4 — Substrate
+// Step 4 — Register MU in SEI (Signal Ecology)
+const sei = registerSpecies(mu);
+
+// Step 5 — Substrate
 const substrateResult = processSignal(mu.payload.raw);
 
-// Step 5 — Actuator
+// Step 6 — Actuator
 const envelope = actuatorEnvelope(substrateResult);
 
-// Step 6 — Print full pipeline
+// Step 7 — Print full pipeline (single, correct output)
 console.log(JSON.stringify({
   mue,
   mu,
   registry,
+  sei,
   substrate: substrateResult,
   actuator: envelope
 }, null, 2));