fix(javascript): preserve analysis applicability after interruption (#4207)

Preserve applicable artifact processing phases and entered/unvisited status after interruption. Centralize JavaScript semantic applicability for full and incremental builders; retain native byte identity, actual JavaScript unknowns and structured-file provenance.

Fixes #3948. Part of #4027.

Validation:78 distinct focused cases across10files, full static/docs, and real Joplin timeout/default public CLI/MCP controls passed. Source pins, every attempt/outlier and compact resource/token projections are retained. No target/native provider execution or speedup claim.

Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>

src/application/javascript/JavaScriptSemanticGraphBuilder.ts

@@ -163,7 +163,7 @@ export interface JavaScriptSemanticGraphProjection {
   readonly adoptFileProjection: (
     projection: JavaScriptSemanticFileProjection,
   ) => void;
-  /** Preserve source-bound unknowns for an execution or result-retention failure. */
+  /** Preserve JavaScript-source unknowns; other file kinds have no semantic module. */
   readonly recordUnavailableFile: (
     file: JavaScriptArtifactFile,
     reason: string,
@@ -346,6 +346,9 @@ export const createJavaScriptSemanticGraphProjection = (
       if (projection.truncated) truncatedFiles += 1;
     },
     recordUnavailableFile: (file, reason, limits, unknownReason) => {
+      // Both full and incremental construction enter here. Metadata/native
+      // processing gaps belong to the application graph, never JavaScript IR.
+      if (file.kind !== "javascript") return;
       const retainedLimits = javaScriptAnalysisCoverageLimits(limits);
       for (const limit of retainedLimits) {
         executionLimits.set(