feat(javascript): analyze selected application sources

Analyze exact selected sources in first-request order before unrelated
static scopes, preserving full artifact identity and byte verification.
Retain selection in CLI/MCP Evidence and summaries, with explicit unknowns
and partial coverage for unselected sources. Keep default full analysis.

Fixes #1848

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>
Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>

src/application/javascript/JavaScriptSemanticGraphBuilder.ts

@@ -130,6 +130,16 @@ export const buildJavaScriptSemanticGraph = ({
   for (const analyzed of analysis.files) {
     if (analyzed.semantic !== null)
       projection.projectFile(analyzed.file, analyzed.semantic.ir);
+    else if (
+      !analyzed.file.text.included &&
+      analyzed.file.text.reason === "outside-analysis-scope"
+    )
+      projection.recordUnavailableFile(
+        analyzed.file,
+        "Source was not analyzed because it is outside the caller-selected source_paths.",
+        null,
+        "incomplete-module",
+      );
   }
   return projection.finish(rootArtifactSha256, applicationGraph);
 };