fix(dedup): preserve same-source node attributes

[Synvoya]

Summary

• retain non-conflicting attributes when exact-ID nodes from the same source file collapse
• preserve the deterministic collision survivor for conflicting values
• keep cross-file references and genuine slugged-path ID collisions isolated
• document the dedup-enabled build contract

Fixes #2091.

Root cause

The exact-ID pre-dedup pass selected one complete node dictionary and discarded the other. That made deterministic collision ranking work, but it also removed complementary AST/semantic data such as summary and confidence_score before NetworkX could merge attributes.

The fix gap-fills only missing keys from same-source duplicates. It does not import attributes from another source file, so the existing #1504 collision boundary remains intact.

Impact

Default dedup=True builds now retain AST precision (source_location, _origin) and semantic enrichment (summary, confidence_score) on the surviving node. Existing survivor values still win genuine conflicts.

Validation

• reproduced Default dedup=True discards a same-ID node's attributes instead of merging them — LLM semantic summaries are silently lost #2091 on current v8 before the fix: summary=None, confidence_score=None
• pytest tests/test_dedup.py -q --tb=short on Python 3.10: 48 passed
• pytest tests/ -q --tb=short on Python 3.12: 3553 passed, 3 skipped
• ruff check graphify/dedup.py graphify/build.py tests/test_dedup.py
• all five tools.skillgen CI checks
• graphify update .

[safishamsi]

Thanks @Synvoya. This shipped in v0.9.24. Your commit was cherry-picked onto v8 (5a4b207) to preserve your authorship, with a follow-up making the gap-fill order-independent and gating it on source_file. Closed-unmerged here, but it is in the release: https://github.com/Graphify-Labs/graphify/releases/tag/v0.9.24