docs: KNOWN_ISSUES dedup (379->240) + Bootstrap external review + E11/E14 harness

[ManSio]

Summary

• KNOWN_ISSUES.md dedup: 16 duplicate auto-sync blocks removed (379 -> 240 lines, 29 entries), header annotated per \scripts/check_known_issues.py\ (R1 compliance).
• AGENT_DIARY.md: resume entry for INC-6C62 (IndexProjectRunner resume-incremental).
• ISSUE.md: add Bootstrap Pipeline external review (2026-09-20, research-opinion, values unverified); fix accidental leading-space indentation on KI-R11 + Порядок выполнения.
• chore(experiments): commit E11 AST/Graph-hybrid re-ranking harness (already referenced by EXPERIMENTS_LOG), E14 real-path embedder repro, embed bench scripts, and text-chunk eval (\scripts/eval_text_chunks.py).

Note on history

PR #37 was merged as squash \

[coderabbitai]

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