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GRAPH_REPORT.md's Knowledge Gaps section always offered undocumented components as a possible explanation for an isolated node, regardless of whether the graph could ever actually have one. That phrase only means anything when a semantic layer exists, document, paper or image nodes an LLM extracted meaning from, where an isolated node genuinely could be mentioned but never explained further. A code only graph has no such nodes at all, so offering it as a live possibility on every report is misleading. The reason now checks whether any node in the graph carries a document, paper or image file_type before including that clause, using the same VALID_FILE_TYPES distinction validate.py already draws between the semantic layer and code/rationale/concept nodes, so no new build time flag is needed. Fixes issue 3801.