File Locations Summary¶
Chapter 11 of the ResearchTools manual. Back to table of contents.
All agents, commands, and skills live under this repository's .claude/ directory.
ResearchTools\
└── .claude\
├── agents\ (18 agents; not all listed below -- see the
│ Agents chapter for the current, complete list)
│ ├── scopus-researcher.md ← /litreview
│ ├── litreview-updater.md ← /litupdate
│ ├── scopus-auditor.md ← /auditreview
│ ├── paper-auditor.md ← /auditpaper
│ ├── thesis-auditor.md ← /auditthesis
│ ├── thesis-proposal-auditor.md ← thesis-proposal audit
│ ├── reviewer-response.md ← /replyreviewer
│ ├── bib-cleaner.md ← /bibclean
│ ├── submit-checker.md ← /submitcheck
│ ├── word-to-latex.md ← /word2latex
│ ├── talk-builder.md ← /talk
│ ├── cover-paper.md ← submission package
│ ├── thesis-to-paper.md ← thesis + conf papers -> journal manuscript
│ ├── authoring-loop.md ← ScholarEval-gated authoring loop
│ ├── latex-writer.md ← LaTeX authoring
│ ├── local-writer.md ← local docs/comments (bridge)
│ ├── local-coder.md ← local code gen (bridge)
│ └── narrative-cv-writer.md ← /cv
├── commands\ (25 commands; not all listed below -- see the
│ Commands chapter for the current, complete list)
│ ├── concis.md ├── slim.md ├── focus.md ├── ctx.md
│ ├── tikz.md ├── test.md ├── doc.md ├── latex.md
│ ├── ref.md ├── litreview.md ├── litupdate.md
│ ├── auditreview.md ├── auditpaper.md
│ ├── auditthesis.md ├── bibclean.md
│ ├── submitcheck.md ├── replyreviewer.md
│ ├── word2latex.md ├── geolocalisation.md
│ ├── loopdev.md ├── talk.md
│ ├── recommendation-letter.md
│ └── cv.md
├── rules\ (code-style, preferences, security, testing, workflows)
└── skills\ (18 skills; not all listed below -- see the
Skills chapter for the current, complete list)
├── scopus\
│ ├── SKILL.md
│ └── scripts\ (scopus_api.py, semantic_scholar_api.py, download_pdf.py,
│ bib_batch.py, litreview_update.py,
│ gemini_reviewer.py, github_reviewer.py, gemini_table.py)
├── scientific-writing\SKILL.md
├── scholar-evaluation\SKILL.md (+ scripts\calculate_scores.py)
├── deliberation\SKILL.md (+ scripts\deliberate.py)
├── extract-statistic\SKILL.md (+ scripts\extract_text.py [--stats-scan / --section-scan];
│ references\statistical-audit-protocol.md, domain-profiles.md)
├── extract-futureworks\SKILL.md (no script; reuses extract_text.py --section-scan;
│ references\futureworks-protocol.md, section-cues.md)
├── word2latex\SKILL.md (+ scripts\docx_inspect.py, manuscript_bib.py)
├── drawio2tikz\SKILL.md (+ scripts\drawio2tikz.py;
│ references\conversion-rules.md)
├── geolocalisation\SKILL.md (+ scripts\extract_locations.py, generate_geomap.py,
│ Test\test_extract_locations.py; references\geocoding-protocol.md;
│ data\ Natural Earth gazetteer cache)
├── loop-engineer\SKILL.md (+ scripts\loop_engineer.py [Agent SDK driver],
loop_audit.py [code-quality scorer], Test\test_loop_audit.py;
references\ LOOP/STATE/PROCESS/ledger templates; requirements.txt)
├── recommendation-letter\SKILL.md (+ scripts\generate_letter.py, letter_templates.py,
│ Test\test_generate_letter.py; references\quality-patterns.md; evals\)
├── narrative-cv\SKILL.md (+ scripts\cv_common.py, cv_inventory.py, cv_select.py,
│ cv_build.py, contribution_types.json,
│ Test\test_cv_common.py, test_cv_inventory.py, test_cv_select.py, test_cv_build.py)
├── paper2talk\SKILL.md (+ scripts\talk_rules.py, talk_model.py, talk_template.py,
fig_export.py, talk_render.py, talk_notes.py, to_a4.py, talk_validate.py,
talk_pptx.py, paper_extract.py, talk_doctor.py,
requirements.txt, Test\ [13 offline suites];
assets\deck_skeleton.js, beamer_skeleton.tex.j2, web_skeleton.html.j2;
references\renderer-contracts.md, qa-loop.md)
├── latex-hygiene\SKILL.md (+ scripts\tex_check.py, tex_common.py, tex_chars.py,
tex_braces.py, tex_par.py, tex_citecov.py, tex_abstract.py, tex_wc.py,
tex_aiscan.py, tex_aiscan_text.py, tex_patch.py, tex_scan.py, tex_build.py,
Test\test_tex_check.py, Test\test_tex_patch.py, Test\test_tex_build.py)
└── opt-local-vram-llm\SKILL.md (+ scripts\vram_probe.py, vram_modelfile.py,
vram_daemon.py, vram_optimizer.py, Test\test_vram_probe.py,
Test\test_vram_modelfile.py, Test\test_vram_daemon.py,
Test\test_vram_optimizer.py)