Add repeat motif functionality and enhance sequence input handling

- Introduced repeat motif management with read and write functions.
- Updated SequenceInput to allow motif settings adjustments.
- Enhanced SequenceAnnotator to utilize repeat motifs for auto-annotation.
- Modified PartSwapper to exclude auto-annotated parts from the library.
- Improved type definitions to support new features.
- Adjusted Vite configuration for dynamic port assignment.

Author: cborac

frontend/src/App.tsx

@@ -5,6 +5,7 @@ import SequenceAnnotator from './components/SequenceAnnotator';
 import ResultsView from './components/ResultsView';
 import PartSwapper from './components/PartSwapper';
 import type { Region, ScrambleResult, WorkSession } from './types';
+import { readRepeatMotif, writeRepeatMotif } from './repeat';
 
 const FAST_MODE_ENABLED = false
 
@@ -15,6 +16,13 @@ export default function App() {
   const [result, setResult] = useState<ScrambleResult | null>(null);
   const [loadedSession, setLoadedSession] = useState<WorkSession | null>(null);
   const [fastMode, setFastMode] = useState(false);
+  const [repeatMotif, setRepeatMotif] = useState<string>(() => readRepeatMotif());
+
+  const handleRepeatMotifChange = (motif: string) => {
+    const m = motif.toUpperCase();
+    setRepeatMotif(m);
+    writeRepeatMotif(m);
+  };
 
   const handleSequenceNext = (seq: string) => {
     setSequence(seq);
@@ -79,14 +87,22 @@ export default function App() {
         </>}
 
         {active === 0 && (
-          <SequenceInput sequence={sequence} onNext={handleSequenceNext} onAssemble={handleAssembleNext} onLoadSession={handleLoadSession} />
+          <SequenceInput
+            sequence={sequence}
+            onNext={handleSequenceNext}
+            onAssemble={handleAssembleNext}
+            onLoadSession={handleLoadSession}
+            repeatMotif={repeatMotif}
+            onRepeatMotifChange={handleRepeatMotifChange}
+          />
         )}
         {active === 1 && (
           <SequenceAnnotator
             sequence={sequence}
             regions={regions}
             onBack={() => setActive(0)}
             onNext={handleAnnotateNext}
+            repeatMotif={repeatMotif}
           />
         )}
         {active === 2 && (

frontend/src/components/PartSwapper.tsx

@@ -241,8 +241,12 @@ export default function PartSwapper({ sequence, regions, result, onResultChange,
 
   useEffect(() => {
     if (!baseResult) return;
+    // Parts annotated via auto-annotate are flagged to stay out of the library.
+    const excluded = new Set(
+      regions.filter(r => r.excludeFromLibrary).map(r => r.name)
+    );
     for (const r of baseResult.regions) {
-      if (r.type === 'part') addToLibrary(r.name, r.aa);
+      if (r.type === 'part' && !excluded.has(r.name)) addToLibrary(r.name, r.aa);
     }
   }, []); // eslint-disable-line react-hooks/exhaustive-deps