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

docs/javascript-application-workflows.md

@@ -347,6 +347,11 @@ remain `changed` while retaining any separate relationship uncertainty.
 An unknown item with no observed content, property, or relationship difference
 does not emit a `changed_from` edge; its pairing and uncertainty remain in the item.
 
+Within a valid `file_occurrence`, `container_sha256` records provenance and does
+not by itself count as a semantic property change. The graph retains the original
+occurrence; its path and source digest still participate in comparison.
+Unrecognized occurrence metadata remains part of property comparison.
+
 One-sided absence is `added` or `removed` only when the opposite input graph has
 complete coverage. With partial, unavailable, or truncated input, the same
 condition is `unknown`. The comparison retains every classified item and