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jordan-gibbs/hyperresearch

Agent-driven research knowledge base. Agents collect, search, and synthesize web research into a persistent, searchable wiki.

Python★ 2,740+153 that day#12 on trending

Analyzed September 12, 2026 at 1367c9b (main) with jscpd 5.4.0 in 0.1s.

3.79%duplicated code · 1,091 of 28,795 lines

98clones in code

108code files of 294 scanned

6.01%duplicated over all files · 223 clones

The code number leaves out tests, fixtures, docs, examples, data files, styles, translations and vendored code, and 1 generated file: src/hyperresearch/indexgen/__init__.py.

Largest clones in the code

10 lines in 9 placespython59 tokens

src/hyperresearch/cli/archive.py:110–119src/hyperresearch/cli/assets.py:20–29src/hyperresearch/cli/citecheck_cmd.py:29–38src/hyperresearch/cli/embed_cmd.py:24–33src/hyperresearch/cli/graph.py:304–313and 4 more

110from hyperresearch.core.vault import Vault, VaultError
111
112try:
113    vault = Vault.discover()
114except VaultError as e:
115    if json_output:
116        output(error(str(e), "NO_VAULT"), json_mode=True)
117    else:
118        console.print(f"[red]Error:[/] {e}")
119    raise typer.Exit(1)

11 lines in 8 placespython60 tokens

src/hyperresearch/cli/assets.py:19–29src/hyperresearch/cli/assets.py:80–90src/hyperresearch/cli/embed_cmd.py:58–68src/hyperresearch/cli/git_cmd.py:33–43src/hyperresearch/cli/import_cmd.py:20–30and 3 more

19"""List downloaded assets (images, screenshots, PDFs)."""
20from hyperresearch.core.vault import Vault, VaultError
21
22try:
23    vault = Vault.discover()
24except VaultError as e:
25    if json_output:
26        output(error(str(e), "NO_VAULT"), json_mode=True)
27    else:
28        console.print(f"[red]Error:[/] {e}")

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10 lines in 8 placespython52 tokens

src/hyperresearch/core/hooks.py:129–138src/hyperresearch/core/hooks.py:347–356src/hyperresearch/core/hooks.py:623–632src/hyperresearch/core/hooks.py:750–759src/hyperresearch/core/hooks.py:1371–1380and 3 more

129depth packet becomes a weak draft section.
130
131## Inputs (from the parent agent)
132
133The spawn prompt may end with a `## Run directives` block — posture
134(register / domain notes / inference depth) auto-selected for this run
135in step 1. It is BINDING and wins wherever it adjusts a default in this
136prompt. No block = this prompt's defaults apply unchanged.
137
138- **research_query**: the user's original question, verbatim. GOSPEL.

347reading of the evidence.
348
349## Inputs (from the parent agent)
350
351The spawn prompt may end with a `## Run directives` block — posture
352(register / domain notes / inference depth) auto-selected for this run
353in step 1. It is BINDING and wins wherever it adjusts a default in this
354prompt. No block = this prompt's defaults apply unchanged.
355
356- **locus**: the full locus object from the loci-analyst output (name,

7 more

10 lines in 7 placespython54 tokens
src/hyperresearch/cli/assets.py:22–31 src/hyperresearch/cli/citecheck_cmd.py:31–40 src/hyperresearch/cli/embed_cmd.py:26–35 src/hyperresearch/cli/link.py:30–39 src/hyperresearch/cli/sources.py:116–125and 2 more
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src/hyperresearch/core/hooks.py:627–632 src/hyperresearch/core/hooks.py:754–759 src/hyperresearch/core/hooks.py:870–875 src/hyperresearch/core/hooks.py:2545–2550 src/hyperresearch/core/hooks.py:3212–3217
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src/hyperresearch/cli/assets.py:22–32 src/hyperresearch/cli/fetch.py:234–244 src/hyperresearch/cli/fetch_batch.py:54–64 src/hyperresearch/cli/graph.py:306–316
22 lines in 2 placespython168 tokens
src/hyperresearch/core/db.py:19–40 src/hyperresearch/core/migrations.py:122–143
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src/hyperresearch/cli/escalation_cmd.py:219–229 src/hyperresearch/cli/escalation_cmd.py:242–252 src/hyperresearch/cli/escalation_cmd.py:266–276
23 lines in 2 placespython136 tokens
src/hyperresearch/cli/note.py:46–68 src/hyperresearch/cli/note.py:309–331
22 lines in 2 placespython134 tokens
src/hyperresearch/core/db.py:143–164 src/hyperresearch/core/migrations.py:219–239

Largest clones over all files, tests and data included

183 lines in 2 placesmarkdowndocs and examples2,882 tokens

src/hyperresearch/skills/hyperresearch.md:105–287tests/fixtures/golden_prompts/skills/hyperresearch.md:105–287

105   For a standard run, pass the installed gear (`<< p.name >>`) unless the user asked for something else.
106   Pass `--budget <usd>` when the user set a spend ceiling. This scaffolds `research/runs/<vault_tag>/` (with `temp/`) and writes `run.json` — the run manifest…
107
1083. **Persist the query file.** Write the verbatim canonical query to `research/runs/<vault_tag>/query.md`:
109   ```markdown
110   ---
111   vault_tag: <slug>
112   created: <ISO-8601 timestamp>
113   source: prompt.txt | user-prompt
114   ---

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152 lines in 2 placesmarkdowndocs and examples994 tokens

src/hyperresearch/skills/hyperresearch-16-readability-audit.md:15–166tests/fixtures/golden_prompts/skills/hyperresearch-16-readability-audit.md:15–166

15# Step 16 — Readability audit & selective apply (FINAL STEP)
16
17**Tier gate:** Runs for ALL tiers. Every report gets a readability audit, regardless of tier — readability is the dimension where small structural changes (par…
18
19**Goal:** improve the report's visual structure, paragraph rhythm, and scannability without changing substantive content. The recommender writes a JSON list of…
20
21**Why split recommender + orchestrator-applied:** an Edit-based reformatter (V7-style) sometimes makes changes that hurt the argument — converting a flowing pa…
22
23---
24

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61 lines in 2 placesmarkdowndocs and examples982 tokens

src/hyperresearch/skills/hyperresearch-2-width-sweep.md:16–76tests/fixtures/golden_prompts/skills/hyperresearch-2-width-sweep.md:16–76

16**Goal:** achieve comprehensive topical coverage — every atomic item from the decomposition must have at least 3 supporting sources by the end of this step. Ta…
17
18---
19
20## Recover state
21
22Read these inputs:
23- `research/runs/<vault_tag>/scaffold.md` — vault_tag (in Run config), modality
24- `research/runs/<vault_tag>/prompt-decomposition.json` — atomic items, sub_questions, entities, pipeline_tier
25- `research/runs/<vault_tag>/temp/coverage-matrix.md` — verbatim query phrases mapped to atomic items

First 10 of 61 lines.

39 lines in 2 placesmarkdowndocs and examples667 tokens
src/hyperresearch/skills/hyperresearch-10-triple-draft.md:62–100 tests/fixtures/golden_prompts/skills/hyperresearch-10-triple-draft.md:62–100
74 lines in 2 placesmarkdowndocs and examples649 tokens
src/hyperresearch/skills/hyperresearch-5-depth-investigation.md:34–107 tests/fixtures/golden_prompts/skills/hyperresearch-5-depth-investigation.md:34–107

By format, code only

Format	Files	Lines	Clones	Duplicated lines	Duplication
python	98	27,977	98	1,091	3.9%
bash	9	644	0	0	0%
perl	1	174	0	0	0%

By format, all files

Format	Files	Lines	Clones	Duplicated lines	Duplication
python	159	43,653	163	1,707	3.91%
markdown	49	8,586	46	1,382	16.1%
yaml	43	578	6	51	8.82%
bash	19	754	4	29	3.85%
text	13	310	3	90	29.03%
json	7	155	1	11	7.1%
toml	2	189	0	0	0%
perl	1	174	0	0	0%
sql	1	22	0	0	0%

Trending appearances

Day	Rank	Stars	Files	Lines	Clones	All files	Code	Health	Commit
Sep 12, 2026	#12	2,740 (+153)	294	54,421	223	6.01%	3.79%	—	`1367c9b`

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