fix(update): preserve surviving hyperedges

[oleksii-tumanov]

Summary

• preserve existing hyperedges during watcher/AST-only graphify update reconciliation when their source file is re-extracted but their member nodes still survive
• keep deletion and dangling-member pruning behavior unchanged
• cover full update and incremental doc update paths

Fixes #1755

Result

Regression fixture keeps the doc-sourced semantic hyperedge after a no-op update:

Before: graphify update removed doc_flow_group
After:  graphify update keeps doc_flow_group -> [doc, doc_design]

Testing

• uv run --frozen pytest tests/test_watch.py -q -k hyperedges (2 passed, 56 deselected)
• uv run --frozen pytest tests/ -q --tb=short (3137 passed, 3 skipped)
• uv run --frozen ruff check graphify/watch.py tests/test_watch.py (passed)
• uv run --frozen python -m tools.skillgen --check (134 artifacts matched)
• uv run --frozen graphify update . (rebuilt graph.json and GRAPH_REPORT.md; no tracked changes)

[safishamsi]

Merged on v8, authored to you. Verified: reproduced the loss (doc-sourced hyperedge dropped on update after a full build), confirmed your fix scopes eviction to deleted/symlink-outside sources so an AST-only rebuild preserves hyperedges whose members survive, and that a real code change which rewrites the graph keeps the hyperedge. Replacement-by-id and dangling-member cleanup stay intact. Full watch suite (58) green incl. your parametrized full/incremental test. Thanks — clean root-cause and minimal fix.