Enforce sequential execution of all 6 phases with file-based gate
checks between each phase transition. Phases 3 (Deep Dive) and 4
(Code & Tools) are marked as mandatory with DO NOT SKIP warnings.
Phases 5 and 6 now explicitly require prior phase outputs to exist
before starting.
6-phase pipeline for discovering, evaluating, and deeply analyzing
GitHub repositories related to a research topic. Reads deep-research
output, discovers repos from multiple sources (GitHub search, code
search, Papers With Code), scores and ranks them, clones and analyzes
code, then produces cross-repo comparison and integration blueprints.
13 Python scripts (stdlib-only), 1 SKILL.md, 1 phase-guide reference.
npx skills parser fails on space-separated argument-hint values.
Changed 12 skills from two-arg hints (e.g., [action] [file]) to single-arg.
Added YAML frontmatter to deep-research (was missing entirely).
All 30 skills now discoverable by npx skills add.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Full academic paper lifecycle coverage: literature search, idea generation,
experiment design, data analysis, figure/table generation, paper writing,
LaTeX formatting, compilation, self-review, revision, slides, and more.
- 29 new skill directories with SKILL.md, scripts/, and references/
- 27 Python scripts + 7 CJS scripts across 15 skills
- All scripts: argparse CLI, docstring headers, stdlib-only where possible
- All 30 SKILL.md files have Related Skills sections (navigable skill graph)
- Updated install.sh: verifies all 30 skills, checks deps, validates scripts
- Updated README.md: documents all skills organized by pipeline phase
- Synced deep-research changes (SKILL.md, api-reference, workflow-phases)
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Documents the two-step install process:
1. npx skills add (global) for the skill + scripts
2. install.sh for the /research command + dependencies
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Packaged deep-research skill for distribution as an installable GitHub repo.
- SKILL.md with YAML frontmatter and user configuration section
- 7 Python scripts (search, download, extract, db, bibtex, compile)
- 3 reference docs (API guide, note templates, workflow phases)
- /research command definition
- install.sh for command installation and dependency checks
- All hardcoded user paths replaced with portable ~ paths
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Lingzhi Yang