fix(extract): create json_config reference target nodes

[oleksii-tumanov]

Summary

• Create real concept nodes for json_config dependency and extends targets before emitting imports / extends edges.
• Add regression coverage that the issue fixture has no dangling endpoints and that build_from_json keeps the edges.

Fixes #1764

Result

dangling_endpoint_edges: 0
kept_edges: [('extends', './tsconfig.base.json'), ('imports', 'bats'), ('imports', 'left-pad')]

Testing

• pytest tests/test_extract.py -q -k 'json' (14 passed, 104 deselected)
• pytest tests/test_manifest_ingest.py tests/test_extract.py -q -k 'manifest or json' (22 passed, 104 deselected)
• ruff check graphify/extractors/json_config.py tests/test_extract.py (passed)
• python -m tools.skillgen --check (passed)
• pytest tests/ -q --tb=short (3136 passed, 3 skipped)
• graphify update . (completed; graph.json and GRAPH_REPORT.md updated locally, no tracked graph output changes)

[safishamsi]

Merged on v8, authored to you. Verified: on package.json + tsconfig.json, the imports/extends edges previously dangled (build dropped them silently); with the fix the targets exist as concept nodes (left-pad, bats, ./tsconfig.base.json), zero dangling endpoints, no self-loops. Full suite 3138 passed. Good catch — this was invisible except via diagnose_extraction. Thanks.