docs: polish README and remove obsolete root-level scripts

Author: ppon1086

README.md

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+Push and commit from only this folder.

THIS_IS_THE_GIT_REPO..txt

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+# Ragcitecheck instability examples
+
+- Evidence key: **doc**
+- Runs: runA, runB
+- Queries evaluated: 3
+- Flip threshold: J < 0.5
+- Min-overlap (stability): 0.5
+- allow_missing: False
+- topk: None
+
+## q1
+- min_overlap_across_pairs: **0.333**
+- worst_pair: **runA vs runB**
+
+| run_id | cited_docs (set) |
+|---|---|
+| runA | d1, d2 |
+| runB | d1, d4 |
+
+- worst-pair diff `runA` → `runB`: J=0.333, flip=YES, +[d4] -[d2]
+
+## q2
+- min_overlap_across_pairs: **1.000**
+- worst_pair: **N/A**
+
+| run_id | cited_docs (set) |
+|---|---|
+| runA | d3 |
+| runB | d3 |
+
+
+## q3
+- min_overlap_across_pairs: **1.000**
+- worst_pair: **N/A**
+
+| run_id | cited_docs (set) |
+|---|---|
+| runA | (empty) |
+| runB | (empty) |
+

cli.py

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+config_a,config_b,avg_overlap,flip_rate,null_rate_a,null_rate_b,null_loss_rate_a_to_b,null_gain_rate_a_to_b,stable_at_min_overlap_0.5
+runA,runB,0.777778,0.333333,0.333333,0.333333,0.000000,0.000000,1

out_report_doc/doc/citation_overlap_hist.png

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+query_id,min_overlap_across_pairs,worst_pair,stable_at_min_overlap_0.5
+q1,0.333333,runA vs runB,0
+q2,1.000000,N/A,1
+q3,1.000000,N/A,1

out_report_doc/doc/instability_examples.md

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+{
+  "allow_missing": false,
+  "baseline": null,
+  "canonicalization": {
+    "collision_count": 0,
+    "collisions": null,
+    "mapped_count": 0,
+    "unmapped_count": 0
+  },
+  "evidence_key": "doc",
+  "flip_threshold": 0.5,
+  "min_overlap": 0.5,
+  "out_dir": "out_report_doc\\doc",
+  "pairwise_rows": 1,
+  "query_count": 3,
+  "run_ids": [
+    "runA",
+    "runB"
+  ],
+  "runs_dir": "tests\\fixtures\\runs_min",
+  "topk": null,
+  "warnings": [
+    "run[0] 'runA' null-citation rate is 33.3% (1/3 queries have empty docs list).",
+    "run[1] 'runB' null-citation rate is 33.3% (1/3 queries have empty docs list)."
+  ]
+}

out_report_doc/doc/pairwise_config_stability.csv

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+run_id,top_k,chunk_size,chunk_overlap
+runA,,,
+runB,,,

out_report_doc/doc/per_query_stability.csv

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+run_id,citation_rate,null_rate,avg_cited_docs,median_cited_docs,p95_cited_docs
+runA,0.666667,0.333333,1.000000,1.000,2.000
+runB,0.666667,0.333333,1.000000,1.000,2.000