watch: 0.4.3 merge fix still drops cross-type edges and loses code nodes

[Joseph94m]

@safishamsi - follow up #253

What 0.4.3 fixed

The 0.4.3 merge logic now loads the existing graph.json, identifies code nodes by file_type == "code", and preserves non-code nodes (doc, image, paper) and their mutual edges. It also preserves hyperedges. Before 0.4.3, the watcher did a full overwrite and everything semantic was destroyed (0 INFERRED, 0 doc nodes, 0 hyperedges). That part is now working:

• Doc nodes: 92 -> 92 (preserved)
• Image nodes: 6 -> 6 (preserved)
• Hyperedges: 11 -> 11 (preserved)

What 0.4.3 did NOT fix

Two problems remain:

1. Cross-type edges (code <-> doc) are dropped

The edge filter in _rebuild_code keeps only edges where neither endpoint is a code node:

sem_edges = [e for e in existing.get("edges", [])
             if e.get("source") not in code_ids and e.get("target") not in code_ids]

Most INFERRED edges connect a code node to a doc node (e.g. a doc explaining a function's rationale). These are all dropped because one endpoint is always a code ID.

Suggested fix - preserve any edge that is INFERRED/AMBIGUOUS, plus pure semantic edges:

sem_edges = [e for e in existing.get("edges", [])
             if e.get("confidence") in ("INFERRED", "AMBIGUOUS")
             or (e.get("source") not in code_ids and e.get("target") not in code_ids)]

Note: I am not 100% sure about the unintended effect these changes may have.

2. AST re-extraction produces fewer code nodes than full pipeline

Full /graphify . found 506 code nodes. The watcher rebuild found only 423 (-83). Most of the loss is .vue file nodes (28 -> 5) and their child functions (139 -> 74 sourced from .vue). The watcher's file discovery may differ from the full pipeline's detection step.

Reproduction (0.4.3 confirmed)

pip show graphifyy  # Version: 0.4.3

1. Run /graphify . on a mixed repo (Go + TypeScript + Vue + markdown docs)
2. Record baseline
3. Start python3 -m graphify.watch . --debounce 3
4. Edit one .ts file and save
5. Compare graph

Metric	Before watcher	After watcher	Delta
Total nodes	604	521	-83
Code nodes	506	423	-83
Doc nodes	92	92	0
Total links	560	396	-164
EXTRACTED	532	383	-149
INFERRED	27	13	-14
AMBIGUOUS	1	0	-1
Edges touching doc nodes	98	3	-95
Hyperedges	11	11	0
.vue file nodes	28	5	-23

Expected behavior

After a watcher rebuild:

• Doc/image nodes: unchanged (working)
• Hyperedges: unchanged (working)
• INFERRED/AMBIGUOUS edges: unchanged (broken - lost 14/1)
• Cross-type edges (code <-> doc): unchanged (broken - lost 95)
• Code node count: same as full pipeline (broken - lost 83)