fix(reference): preserve source scope and loader authority

Share parser-owned package and runtime facts across dependency consumers.
Preserve uncertain loader requests and explicit wrapper bindings without
inventing unbound require authority in known modules. Cover selected source
grammar through the public MCP boundary and retain ambient/type dependencies.

Open each selected directory before loading its scoped policy, retaining
partial directory failures and cleanup ownership. Preserve explicit caller
negation precedence and source diagnostics across inventory projections.

Clarify how version comparison retains container provenance without claiming
semantic drift. Use independent unknown source inputs to keep candidate-limit
fixtures meaningful as conditional branch evaluation becomes more precise.

Fixes #6891
Fixes #6882
Fixes #6883
Fixes #6859

src/application/ReferenceSourceImportEntries.test.ts

@@ -162,7 +162,7 @@ it("resolves declared package mains and index fallback from source-owned fields"
       'require("./pkg");\nrequire("./dep");\nrequire("./fallback");\n',
     ],
     [
-      "main.ts",
+      "main.cts",
       'import dep = require("./typed");\n' +
         'require("./typed");\n' +
         'import data = require("./json-package");\n' +
@@ -239,28 +239,28 @@ it("resolves declared package mains and index fallback from source-owned fields"
     parse_state: "parsed",
   });
   expect(parsed.relationships).toContainEqual({
-    from_path: "main.ts",
+    from_path: "main.cts",
     to: "typed/index.ts",
     kind: "requires",
     resolution: "internal",
     parse_state: "parsed",
   });
   expect(parsed.relationships).toContainEqual({
-    from_path: "main.ts",
+    from_path: "main.cts",
     to: "typed.js",
     kind: "requires",
     resolution: "internal",
     parse_state: "parsed",
   });
   expect(parsed.relationships).toContainEqual({
-    from_path: "main.ts",
+    from_path: "main.cts",
     to: "json-package/data.json",
     kind: "requires",
     resolution: "internal",
     parse_state: "parsed",
   });
   expect(parsed.relationships).toContainEqual({
-    from_path: "main.ts",
+    from_path: "main.cts",
     to: "emitted.ts",
     kind: "requires",
     resolution: "internal",