This skill should be used when the user asks to start a new research project, import an existing code-plus-Markdown repository into Obsidian, or bind the current repository to a compact research knowledge base for future syncing.
Scanned 9/3/2026
Install to Claude Code
npx -y skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill obsidian-project-bootstrap --agent claude-codeInstalls into .claude/skills of the current project.
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---
name: obsidian-project-bootstrap
description: This skill should be used when the user asks to start a new research project, import an existing code-plus-Markdown repository into Obsidian, or bind the current repository to a compact research knowledge base for future syncing.
---
# Obsidian Project Bootstrap
Bootstrap a project knowledge base for the current repository.
## Role in the workflow
This is a **supporting skill**.
Use `obsidian-project-memory` as the main workflow authority. Use this skill only when a repository still needs its initial binding or rebuild.
## When to use
- The user says “start a new research project”.
- The user has an existing repo with code plus Markdown and wants an Obsidian knowledge base generated automatically.
- `obsidian-project-memory` detects a research-project candidate but no existing binding.
## Required input
Resolve the vault path from one of:
1. explicit user input,
2. `OBSIDIAN_VAULT_PATH`.
## Procedure
1. Identify the repository root.
2. Run a preflight detect step first:
```bash
python3 "${CLAUDE_PLUGIN_ROOT}/skills/obsidian-project-memory/scripts/project_kb.py" detect --cwd "$PWD"
```
3. Only if the repo is unbound and should be imported, run bootstrap:
```bash
python3 "${CLAUDE_PLUGIN_ROOT}/skills/obsidian-project-memory/scripts/project_kb.py" bootstrap --cwd "$PWD" --vault-path "$OBSIDIAN_VAULT_PATH"
```
4. Verify that bootstrap created at least:
- `.claude/project-memory/registry.yaml`
- `.claude/project-memory/<project_id>.md`
- `Research/{project-slug}/00-Hub.md`
- `Research/{project-slug}/01-Plan.md`
- `Research/{project-slug}/Knowledge/Source-Inventory.md`
- `Research/{project-slug}/Knowledge/Codebase-Overview.md`
5. If the imported project still lacks real background or experiment context, switch to an agent-first pass:
- read the most informative repo docs and code entry points,
- synthesize durable notes into `Knowledge/`, `Papers/`, `Experiments/`, `Results/`, or `Writing/`,
- avoid placeholder notes.
6. Summarize the created knowledge base and the next recommended canonical notes to fill in.
## Notes
- The bootstrap process imports **structure and summaries**, not raw datasets, caches, checkpoints, or the whole code tree.
- Ignore `.git`, `.venv`, `node_modules`, caches, checkpoints, binaries, and other heavy artifacts.
- The default vault is compact: `00-Hub.md`, `01-Plan.md`, `Knowledge/`, `Papers/`, `Experiments/`, `Results/`, `Writing/`, `Daily/`, `Archive/`.
- If `python3` is unavailable in the current shell, use the system Python interpreter that can run `project_kb.py` and say so explicitly.
## References
- `references/BOOTSTRAP-RUNBOOK.md` - preflight decisions, failure modes, and post-bootstrap verification

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