fix(javascript): preserve unresolved version relationships

Keep positive topology differences separate from unpaired neighbor identity. Preserve exact content pairing and source observations, report unresolved relationships without inventing incomplete inventory, and omit comparison edges when no substantive difference was observed.

Validated with 45 focused domain/CLI/MCP tests, nine expanded domain controls, check:fast, and docs:check. Clean baseline fails seven controls and passes two positive controls. Controlled static fixtures only; no target execution or large-bundle profiling.

Refs #4681

docs/javascript-application-workflows.md

@@ -289,7 +289,8 @@ links, limitations, and a `changed_from` graph containing all compared nodes,
 their observations, and relationships.
 
 A matched pair whose only differing dimension is `location` counts as
-`unchanged` when both input graphs have complete coverage. This includes an
+`unchanged` when both input graphs have complete coverage and its neighboring
+relationship identities are resolved. This includes an
 identical module shifted by an earlier bundle edit and a named IPC channel
 observed at a new offset. The item still reports `dimensions: ["location"]`
 and both node IDs; the graph retains both original observations and coordinates.
@@ -298,6 +299,16 @@ Content, property, and complete relationship differences still count as
 retains the location and coverage dimensions. Matching confidence is unchanged:
 an inferred pair is not promoted to exact identity by this classification.
 
+Complete inventory does not resolve ambiguous or unmatched relationship targets.
+A matched module with identical bytes can therefore remain `unknown` when a
+neighbor, including its containing chunk, has no cross-version match. The item
+retains its exact content match, coordinates, candidate inventory, and an explicit
+relationship-identity limitation. `coverage` is added to its dimensions only for
+incomplete inventory. Definite content, property, or complete topology differences
+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.
+
 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