Imbad0202/academic-research-skills

Academic Research Skills for Claude Code: research → write → review → revise → finalize

Python★ 46,084+496 that day#8 on trending

Analyzed September 4, 2026 at 9443623 (main) with jscpd 5.4.0 in 9.6s. Code duplication stayed at 4.22% across 4 appearances since Sep 1.

4.22%duplicated code · 5,484 of 129,922 lines

276clones in code

228code files of 2,302 scanned

6.8%duplicated over all files · 1,953 clones

The code number leaves out tests, fixtures, docs, examples, data files, styles, translations and vendored code.

Largest clones in the code

351 lines in 2 placespython2,155 tokens

scripts/check_re_review_synthesis.py:1956–2306scripts/legacy/check_re_review_synthesis_v1_0.py:1516–1866

1956        "triggering divergence"
1957    )
1958elif row["cross_model_verdict"] == rec["pre_reapplication_verdict"]:
1959    # §6 dispatch order is normative: diverges is identified
1960    # FIRST (judge verdict vs the row's verdict), THEN the
1961    # system intent is emitted and the 2B' call dispatched. A
1962    # judge verdict equal to the dispatch-time pre-value means
1963    # no divergence existed to resolve — the chain manufactures
1964    # its own diverges status after the fact.
1965    fails.add(

First 10 of 351 lines.

144 lines in 2 placespython1,509 tokens

scripts/check_re_review_synthesis.py:719–862scripts/legacy/check_re_review_synthesis_v1_0.py:585–728

719if row["obligation_class"] == "MUST_FIX":
720    if not has_status:
721        v.fail(path, "MUST_FIX rows always carry cross_model_status (§5.3 / #539)")
722elif has_status or has_cmv:
723    v.fail(path, "SHOULD_FIX/CONSIDER rows carry neither cross-model field (#539 scope)")
724if has_status:
725    v.enum(row["cross_model_status"], f"{path}.cross_model_status",
726           ("agree", "diverges", "unavailable", "not_configured"))
727    if row["cross_model_status"] in ("agree", "diverges"):
728        if not has_cmv:

First 10 of 144 lines.

151 lines in 2 placespython1,428 tokens

scripts/check_re_review_synthesis.py:499–649scripts/legacy/check_re_review_synthesis_v1_0.py:386–536

499v.enum(art["contract_version"], "$.contract_version", ("1.1",))
500v.string(art["round_id"], "$.round_id")
501v.pattern(art["precommitment_hash"], "$.precommitment_hash", _SHA256_RE, "sha256 hex")
502v.array(art["items"], "$.items")
503for i, rec in enumerate(art["items"]):
504    path = f"$.items[{i}]"
505    v.obj(rec, path, ["item_id", "verdict", "change_summary", "verified_by", "applied_criterion"],
506          ["evidence_anchor", "cannot_verify_reason", "residual_gap"])
507    v.pattern(rec["item_id"], f"{path}.item_id", _ITEM_ID_RE, "REV-<id>")
508    v.enum(rec["verdict"], f"{path}.verdict", VERDICTS)

First 10 of 151 lines.

7 more

166 lines in 2 placespython949 tokens
scripts/ars_apply_revision_patch.py:242–407 scripts/legacy/ars_apply_revision_patch_v1_0.py:241–406
110 lines in 2 placespython782 tokens
scripts/check_re_review_synthesis.py:211–320 scripts/legacy/check_re_review_synthesis_v1_0.py:173–282
139 lines in 2 placespython670 tokens
scripts/ars_apply_revision_patch.py:103–241 scripts/legacy/ars_apply_revision_patch_v1_0.py:101–239
90 lines in 2 placespython636 tokens
scripts/check_re_review_synthesis.py:1477–1566 scripts/legacy/check_re_review_synthesis_v1_0.py:1058–1142
48 lines in 2 placespython550 tokens
scripts/ars_apply_revision_patch.py:1–48 scripts/legacy/ars_apply_revision_patch_v1_0.py:1–48
90 lines in 2 placespython522 tokens
scripts/check_re_review_synthesis.py:1855–1944 scripts/legacy/check_re_review_synthesis_v1_0.py:1415–1504
57 lines in 2 placespython457 tokens
scripts/check_re_review_synthesis.py:938–994 scripts/legacy/check_re_review_synthesis_v1_0.py:801–857

Largest clones over all files, tests and data included

130 lines in 24 placesjsondata files367 tokens
evals/heldout/reviewer_seeded_defects/runs/raw/2026-08-03-ms00_clean-baseline-r1/contract.json:1–130 evals/heldout/reviewer_seeded_defects/runs/raw/2026-08-03-ms00_clean-baseline-r2/contract.json:1–130 evals/heldout/reviewer_seeded_defects/runs/raw/2026-08-03-ms00_clean-baseline-r99/contract.json:1–130 evals/heldout/reviewer_seeded_defects/runs/raw/2026-08-03-ms02_qual-baseline-r2/contract.json:1–130 evals/heldout/reviewer_seeded_defects/runs/raw/2026-08-04-ms00_clean-baseline-r1/contract.json:1–130and 19 more
```
1{
2  "contract_id": "reviewer/reviewer_full/v2",
3  "mode": "reviewer_full",
4  "stage": "reviewer_full_review",
5  "baseline_version": "v3.20.0",
6  "panel_size": 5,
7  "acceptance_dimensions": [
8    {
9      "id": "D1",
10      "name": "methodology_rigor",
```
First 10 of 130 lines.

349 lines in 2 placesmarkdowndocs and examples4,521 tokens

agents/synthesis_agent.md:8–356deep-research/agents/synthesis_agent.md:8–356

8# Synthesis Agent — Cross-Source Integration & Gap Analysis
9
10## Role Definition
11
12You are the Synthesis Agent. You perform the core intellectual work of research: integrating findings across multiple sources, identifying patterns and contrad…
13
14## Phase Boundary (v3.9.2)
15
16You are a single-phase agent assigned to **Phase 3 (Analysis)**. Your sole deliverable is the Synthesis Report (integrated findings + contradiction resolution …
17

First 10 of 349 lines.

334 lines in 2 placesmarkdowndocs and examples4,204 tokens

agents/report_compiler_agent.md:8–341deep-research/agents/report_compiler_agent.md:8–341

8# Report Compiler Agent — APA 7.0 Academic Report Writer
9
10## Role Definition
11You are the Report Compiler Agent. You transform research findings, synthesis narratives, and methodological blueprints into polished academic reports followin…
12
13## Core Principles
141. **APA 7.0 compliance**: Every element follows APA 7th edition standards
152. **Evidence-based writing**: Every claim must be supported by cited evidence
163. **Reader-centered**: Write for the target audience, not for yourself
174. **Structure drives clarity**: Follow the standard structure — deviations must be justified

First 10 of 334 lines.

291 lines in 2 placesmarkdowndocs and examples3,719 tokens
agents/research_architect_agent.md:8–298 deep-research/agents/research_architect_agent.md:8–298
59 lines in 4 placesmarkdowndocs and examples1,006 tokens
academic-paper-reviewer/agents/devils_advocate_reviewer_agent.md:57–115 academic-paper-reviewer/agents/domain_reviewer_agent.md:56–114 academic-paper-reviewer/agents/eic_agent.md:55–113 academic-paper-reviewer/agents/perspective_reviewer_agent.md:56–114

By format, code only

Format	Files	Lines	Clones	Duplicated lines	Duplication
python	210	126,755	276	5,484	4.33%
bash	16	2,800	0	0	0%
javascript	1	193	0	0	0%
perl	1	174	0	0	0%

By format, all files

Format	Files	Lines	Clones	Duplicated lines	Duplication
python	445	261,892	861	12,540	4.79%
markdown	916	190,849	564	10,020	5.25%
json	504	68,214	446	13,297	19.49%
text	167	7,453	20	251	3.37%
yaml	135	5,929	17	236	3.98%
txt	21	515	16	320	62.14%
diff	22	362	9	77	21.27%
r	2	187	8	53	28.34%
bash	43	4,250	6	119	2.8%
markup	9	2,533	6	156	6.16%

Trending appearances

Day	Rank	Stars	Files	Lines	Clones	All files	Code	Health	Commit
Sep 4, 2026	#8	46,084 (+496)	2,302	545,107	1,953	6.8%	4.22%	—	`9443623`
Sep 3, 2026	#9	45,682 (+799)	2,302	545,107	1,959	6.87%	4.22%	—	`9443623`
Sep 2, 2026	#2	45,097 (+193)	2,302	545,107	1,952	6.8%	4.22%	—	`9443623`
Sep 1, 2026	#2	44,562 (+161)	2,301	545,034	1,953	6.82%	4.22%	—	`e8bf858`

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