flonat-research 0.1.0

package/skills/init-project-research/SKILL.md

@@ -0,0 +1,368 @@
+---
+name: init-project-research
+description: "Use when you need to bootstrap a full research project with directory scaffold and Overleaf symlink."
+allowed-tools: Bash(mkdir*), Bash(ln*), Bash(ls*), Bash(git*), Bash(touch*), Bash(jq*), Bash(uv*), Bash(scout *), Bash(curl*), Bash(wget*), Read, Write, Edit, Glob, Grep, Task, WebSearch, WebFetch, AskUserQuestion
+argument-hint: "[project-name or no arguments for guided setup]"
+---
+
+# Init Project Research
+
+> Interview-driven skill that scaffolds a research project directory, creates an Atlas topic, syncs to vault (Atlas + Pipeline + Venues), and integrates with the user's Task Management system.
+
+## When to Use
+
+- Starting a new research paper or project from scratch
+- When the user says "new project", "set up a project", "init project", "bootstrap project"
+- After deciding to pursue a new research idea that needs its own folder
+- When scaffolding ideas from Scout reports, brainstorming, or supervisor meetings
+
+## Overview
+
+Eight phases, executed in order:
+
+1. **Interview** — gather project details via structured questions
+2. **Scaffold** — create directory structure based on project type
+3. **Seed files** — populate CLAUDE.md, README.md, .gitignore with interview answers
+4. **Overleaf symlink** — link `paper/` to Overleaf directory
+5. **Git init** — initialise repo and make first commit
+6. **Atlas & Pipeline sync** — create Atlas topic file, vault atlas entry, Pipeline row, venue links, Dropbox folder
+7. **Task Management sync** — update context library files
+8. **Literature & Discovery** — run literature review + scout novelty assessment
+9. **Confirmation** — report what was created
+
+---
+
+## Phase 1: Interview
+
+Use `AskUserQuestion` for structured input. Three rounds to avoid overwhelming.
+
+### Pre-Interview: Auto-Detection
+
+Before asking questions, scan the project directory (if it already exists) for metadata:
+- **LaTeX files** — extract `\title{}`, `\author{}`, `\begin{abstract}`, `\begin{keyword}` from `.tex` files
+- **Markdown files** — check for `README.md`, `notes.md` with `# Title` headings
+- **BibTeX files** — note `.bib` presence for later phases
+- **Overleaf symlink** — if `paper/` is a symlink, follow and scan the target
+
+Present detected values as the first option (marked "Detected from paper") in interview questions. Always allow override. If the directory doesn't exist yet, skip auto-detection.
+
+### Round 1 — Core Identity
+
+1. **Project slug** — kebab-case identifier (e.g., `costly-voice`). Folder name on disk is Title Case with spaces (e.g., `Costly Voice`). Confirm the derived folder name.
+2. **Working title** — full paper/project title
+3. **Authors / collaborators** — names and affiliations
+4. **Research area** — which parent folder under Projects/. Scan for existing theme folders and present as options. Also offer "New topic folder" and "Other location".
+5. **Target venue** — journal, conference, or preprint:
+   - **Journal:** Check CABS AJG ranking via `.context/resources/venue-rankings.md` and the CSV (`.context/resources/venue-rankings/abs_ajg_2024.csv`). For SJR score, query the Elsevier Serial Title API (see venue-rankings.md for snippet; requires `SCOPUS_API_KEY`). Flag journals below CABS 4 with alternatives.
+   - **Conference:** Check CORE ranking via `.context/resources/venue-rankings.md` and the CSV (`.context/resources/venue-rankings/core_2026.csv`). Capture page limit, format, review type, anonymisation, deadlines.
+   - **Preprint:** Note the server (arXiv, SSRN) — no ranking check needed.
+6. **Deadline** — submission deadline if known
+
+### Round 2 — Setup Details
+
+1. **Overleaf project** — ask: "Does the Overleaf project already exist, or should I create it?" If it exists, get the folder name under the Overleaf root (read from `~/.config/task-mgmt/overleaf-root`, fallback `~/Apps/Overleaf/`) and verify the path. If it doesn't exist, create it via `mkdir` (creating a folder in the Overleaf root automatically creates an Overleaf project).
+2. **LaTeX template** — scan `Task Management/templates/` for options. Default: Working Paper (`templates/latex-wp/`). Also offer "None".
+3. **Overleaf external sharing link** — read-only URL for collaborators
+4. **Git repository?** — Local git (Recommended) / GitHub remote / No git
+5. **Project type** — Experimental (`code/`, `data/`, `output/`) / Computational (`src/`, `tests/`, `experiments/`, `results/`) / Theoretical (minimal) / Mixed
+
+### Round 3 — Research Content
+
+Paper type, abstract, key research questions, then paper-type-specific questions (empirical/theoretical/methodological/mixed) adapted from Lopez-Lira's idea evaluation template.
+
+Full question set and storage instructions: [`references/interview-round3.md`](references/interview-round3.md)
+
+---
+
+## Phase 1.5: Handle Existing Files
+
+If the target directory already exists with files:
+
+1. Scan for existing files (excluding `.claude/`)
+2. Read documents to understand content
+3. Present a reorganisation plan: keep in place / move to `docs/` / move to `docs/readings/` / move to `paper/` / move to `to-sort/` / absorb into seed files
+4. Wait for approval, execute, double-check before deletions
+5. Use interview content from existing docs to reduce Round 3 questions
+
+If the directory doesn't exist, create it and proceed.
+
+---
+
+## Phase 2: Scaffold Directory
+
+### Naming Convention
+
+- **Slug** (kebab-case): `example-project` — citation keys, git refs
+- **Folder name** (Title Case with spaces): `Example Project` — directory on disk
+
+### Overleaf Separation (Hard Rule)
+
+**`paper/` is for LaTeX source files ONLY.** No code, data, scripts, or computational artifacts. See `.claude/rules/overleaf-separation.md`.
+
+### Common Core (always created)
+
+```
+<Folder Name>/
+├── CLAUDE.md
+├── README.md
+├── MEMORY.md
+├── .gitignore
+├── .context/
+│   ├── current-focus.md
+│   ├── field-calibration.md
+│   └── project-recap.md
+├── .claude/
+│   ├── hooks/
+│   │   └── copy-paper-pdf.sh   # PostToolUse hook — copies paper-*/paper/main.pdf → backup/*_vcurrent.pdf
+│   └── settings.local.json
+├── correspondence/
+│   └── reviews/           # .gitkeep (see scaffold-details.md for review structure)
+├── docs/
+│   ├── literature-review/  # .gitkeep
+│   ├── readings/           # .gitkeep
+│   └── venues/             # .gitkeep (submission/venue material only)
+├── log/                   # .gitkeep
+├── paper/                 # Paper directory (Phase 4):
+│   └── paper/             #   Symlink → Overleaf — LaTeX source ONLY
+│                          #   Venue-specific files (checklists, cover letters) live in parent
+├── backup/                # Local backups of Overleaf paper directories (subdirs per paper)
+├── reviews/               # .gitkeep (subdirs created on demand by review agents)
+└── to-sort/               # .gitkeep
+```
+
+### Conditional Structure
+
+**Experimental** — add: `code/python/`, `code/R/`, `data/raw/`, `data/processed/`, `output/figures/`, `output/tables/`, `output/logs/`
+
+**Computational** — add: `src/<project-name>/` (with `__init__.py`), `tests/`, `experiments/configs/`, `results/`, `output/logs/`, `pyproject.toml`, `.python-version`
+
+**Theoretical** — nothing extra.
+
+**Mixed** — present elements and ask which to include.
+
+**Venues:** When a target venue is known, seed `docs/venues/<venue-slug>/submission/`. For conference venues, also seed a submission checklist. Full venue structure and checklist template: [references/scaffold-details.md](references/scaffold-details.md).
+
+### Python Tooling
+
+**Always use `uv` — never bare `pip`, `python`, or `requirements.txt`.** For computational projects, init with `uv init`. For experimental projects, add `pyproject.toml` when dependencies are first needed.
+
+### Implementation
+
+```bash
+mkdir -p <dir> && touch <dir>/.gitkeep  # Create all directories
+mkdir -p .claude/hooks                   # Create hook, chmod +x
+mkdir -p .claude/state                   # Machine-specific memory (gitignored)
+```
+
+---
+
+## Phase 3: Seed Files
+
+### CLAUDE.md vs README.md
+
+- **CLAUDE.md** — Instructions for Claude: safety rules, folder structure, conventions, symlink paths
+- **README.md** — Human-readable overview: title, authors, abstract, status checklist, links
+
+Both overlap on basic metadata but diverge in purpose. Follow the `lean-claude-md` rule for CLAUDE.md.
+
+### Seed File Templates
+
+Full templates: [`templates/seed-files.md`](templates/seed-files.md)
+
+| File | Purpose |
+|------|---------|
+| `CLAUDE.md` | Claude instructions: overview, venue, RQs, setup, conventions |
+| `README.md` | Human overview: title, authors, abstract, links, status |
+| `.gitignore` | Standard ignores: OS, IDE, data, paper, Python, R, LaTeX |
+| `MEMORY.md` | Knowledge base: notation, estimands, decisions, pitfalls |
+| `.context/current-focus.md` | Initial "just initialised" state |
+| `.context/field-calibration.md` | Per-project domain profile for agents (placeholder template — `/interview-me` Phase 7 populates it) |
+| `.context/project-recap.md` | Research design notes |
+| `.claude/hooks/copy-paper-pdf.sh` | PDF copy hook |
+| `log/YYYY-MM-DD-HHMM-setup.md` | Initial setup log: project name, creation date, scaffold type, next steps |
+| `docs/pipeline-manifest.md` | **(Experimental/Computational only)** Script status, data files, manuscript figure manifest. Template: [`templates/pipeline-manifest.md`](templates/pipeline-manifest.md) |
+| `run_all.sh` | **(Experimental/Computational only)** Multi-language pipeline executor (Python via uv, R, Stata). Template: [`templates/run-all.sh`](templates/run-all.sh). `chmod +x` after creation. |
+
+### Permissions Sync
+
+After writing `.claude/settings.local.json` (with hook config), merge global permissions into it so the new project starts with full permissions from day one:
+
+1. Read `~/.claude/settings.json` → extract `permissions.allow` array
+2. Read the newly created `.claude/settings.local.json`
+3. Compute the union: `local_permissions ∪ global_permissions`
+4. Write the merged `permissions.allow` back to `.claude/settings.local.json` (preserving the `hooks` key)
+
+```bash
+# Merge global permissions into the new project's settings
+jq -s '.[0].permissions.allow as $global |
+  .[1] | .permissions.allow = ((.permissions.allow // []) + $global | unique | sort)' \
+  ~/.claude/settings.json .claude/settings.local.json > .claude/settings.local.json.tmp \
+  && mv .claude/settings.local.json.tmp .claude/settings.local.json
+```
+
+Also merge the `permissions.deny` array using the same logic.
+
+---
+
+## Phase 4: Overleaf Symlink & Template
+
+### Paper Directory Convention (Nested Pattern)
+
+Each paper submission gets its own **real directory** at project root (e.g., `paper/`, `paper-ccs/`, `paper-rg/`). Inside that directory, a `paper/` **symlink** points to the Overleaf folder. This nesting allows venue-specific files (submission checklists, cover letters, response documents, reviewer correspondence) to live alongside the Overleaf content without being synced to Overleaf.
+
+**Structure:**
+```
+paper-ccs/                    # Real directory (venue wrapper)
+├── paper/                    # Symlink → Overleaf directory
+├── submission-checklist.md   # Venue-specific (not in Overleaf)
+├── cover-letter.tex          # Venue-specific
+└── response-to-reviewers.tex # Added after R&R
+```
+
+**Single-paper projects** use the same pattern:
+```
+paper/                        # Real directory (venue wrapper)
+└── paper/                    # Symlink → Overleaf directory
+```
+
+**Naming convention:** `Paper {THEME_PREFIX} {Title Cased Slug}` — e.g., `Paper ASG Privacy Compliance Gaming`, `Paper BDS Identity Belief Alignment`. The theme prefix is a short abbreviation of the research theme:
+
+| Theme | Prefix |
+|-------|--------|
+| Category A | ASG |
+| Category B | BDS |
+| Category C | EnvEcon |
+| Category D | HAI |
+| Industrial Organisation | IO |
+| Mechanism Design | MechDes |
+| NLP & Computational AI | NLP |
+| Operations Research | OR |
+| Category F | OrgStrat |
+| Category G | PolSci |
+
+For multi-venue submissions, append the venue abbreviation in parentheses: `Paper ASG Privacy Compliance Gaming (CCS)`.
+
+**Commands:**
+```bash
+# Create the Overleaf project folder if it doesn't exist yet
+# (creating a folder in the Overleaf root automatically creates an Overleaf project)
+overleaf_root="$(cat ~/.config/task-mgmt/overleaf-root 2>/dev/null || echo ~/Apps/Overleaf)"
+mkdir -p "$overleaf_root/Paper ASG Privacy Compliance Gaming (CCS)"
+
+# For each venue:
+mkdir -p paper-ccs
+ln -s "$overleaf_root/Paper ASG Privacy Compliance Gaming (CCS)" paper-ccs/paper
+
+# Single paper:
+mkdir -p paper
+ln -s "$overleaf_root/Paper BDS Identity Belief Alignment" paper/paper
+```
+
+**Important:** Never rename or delete Overleaf folders — see `.claude/rules/overleaf-separation.md` (Overleaf Folder Lifecycle).
+
+Ensure `.latexmkrc` exists inside the Overleaf target (the symlink destination), not in the wrapper directory. Full template setup: [references/scaffold-details.md](references/scaffold-details.md#overleaf-symlink-commands-phase-4).
+
+### Backup Directory
+
+After creating paper directories, create a `backup/` directory with one subdirectory per paper:
+
+```bash
+mkdir -p backup/
+for d in paper*/; do
+  mkdir -p "backup/$(basename "$d")"
+done
+```
+
+**Convention:** One `backup/` directory at project root, with subdirectories matching each `paper*` directory name. The daily `backup-overleaf-papers.sh` script copies `.tex`/`.bib`/style files from the Overleaf symlink targets into these subdirectories.
+
+**Examples:**
+- Single paper: `backup/paper/`
+- Multi-paper: `backup/paper-ccs/`, `backup/paper-rg/`
+
+---
+
+## Phase 5: Git Init (conditional)
+
+**Skip entirely if the user chose "No git" in Round 2.**
+
+```bash
+cd "<project-path>" && git init && git branch -m main && git add . && git commit -m "Initialize project: <working-title>"
+```
+
+If GitHub remote requested: `gh repo create "user/<project-name>" --private --source=. --remote=origin --push`
+
+If local git only: remind to push before switching machines. **Do NOT push unless a remote was explicitly requested.**
+
+---
+
+## Phase 6: Atlas & Pipeline Sync
+
+Creates the research topic in all systems: local file → vault atlas → vault pipeline → Venues → project folder → documentation.
+
+Full steps (6a–6f) and Atlas defaults: [`references/atlas-pipeline-sync.md`](references/atlas-pipeline-sync.md)
+
+---
+
+## Phase 7: Task Management Integration
+
+All paths relative to Task Management root.
+
+### 7a. Update `.context/projects/_index.md`
+
+Add a new row to the "Papers in Progress" table. Stage is typically "Idea" or "Literature Review".
+
+### 7b. Create `.context/projects/papers/<short-name>.md`
+
+Template in [references/scaffold-details.md](references/scaffold-details.md#papers-context-file-template).
+
+### 7c. Update `.context/current-focus.md`
+
+Add to Top 3 Active Projects or as an Open Loop. Use targeted `Edit` — do NOT rewrite the file.
+
+---
+
+## Phase 8: Literature & Discovery
+
+After scaffolding and syncing, automatically run a literature review (`/literature`) and scout novelty assessment (`/scout`) in parallel via sub-agents.
+
+Full steps (8a–8c) and error handling: [`references/literature-discovery.md`](references/literature-discovery.md)
+
+---
+
+## Phase 9: Confirmation Report
+
+Print the structured confirmation after all phases complete.
+
+Full template: [`references/confirmation-report.md`](references/confirmation-report.md)
+
+---
+
+## Error Handling
+
+- **Overleaf path doesn't exist:** Create symlink anyway (resolves when Overleaf syncs). Warn user.
+- **gh CLI not available:** Skip GitHub, note in report.
+- **taskflow MCP server fails:** Skip vault entry, offer to retry.
+- **Directory already exists:** Ask whether to continue or abort.
+- **Duplicate Atlas slug:** Flag and skip Atlas creation — may need merge into existing topic.
+
+## Never Do These (Atlas)
+
+- Never create a topic file without YAML frontmatter — it breaks RECAP.md generation
+- Never hard-code vault theme paths — always look them up (they change if recreated)
+- Never use Methods values outside the valid multi-select options — the API will reject
+- Never use venue/output names as slugs — the slug names the research idea
+- Never create a separate topic file for a companion paper of an existing idea — add it as an output instead
+
+## Cross-References
+
+| Skill | Relationship |
+|-------|-------------|
+| `/literature` | Runs automatically in Phase 8a — initial literature review |
+| `/scout` | Runs automatically in Phase 8b — novelty assessment |
+| `/project-safety` | Already handled — .gitignore and settings created during init |
+| `/save-context` | Context library entries created during Phase 7 |
+| `/session-log` | Offer to create a session log after init completes |
+| `/interview-me` | To develop the research idea before scaffolding |
+| `/atlas-deploy` | After init, run to compile and deploy changes to atlas.user.com |
+| `/atlas-review` | **Drift trigger:** new projects change theme dir counts — see `atlas-review/references/drift-checks.md` |
+| `references/domain-profile-template.md` | Template for economics/field-specific domain profiles — copy to project's `docs/domain-profile.md` during init for economics papers |

package/skills/init-project-research/references/atlas-pipeline-sync.md

@@ -0,0 +1,70 @@
+# Atlas & Pipeline Sync — Phase 6 Details
+
+> Referenced from: `init-project-research/SKILL.md` Phase 6
+
+Creates the research topic in all systems: local file → vault atlas → vault pipeline → Venues → project folder → documentation.
+
+## 6a. Create Atlas Topic File
+
+1. Read `research/atlas/themes.md` — current themes and topic lists
+2. Glob `research/atlas/topics/**/*.md` — existing slugs (avoid duplicates)
+3. Determine the **slug** (kebab-case, 2-5 words). Pattern: `{contribution}-{domain-object}`. Names the idea, not venue/output/method. Within clusters (e.g., carbon, elicitation), each slug needs a unique distinguishing word. Anti-patterns: acronyms (`efficient-pe`), bare fields (`smart-meters`), venue names (`facct-paper`). Good: `carbon-collusion`, `elicitation-cost-tradeoffs`.
+4. Write `research/atlas/topics/{theme-dir}/{slug}.md` using the YAML frontmatter template from [`atlas-schema.md`](atlas-schema.md). Include `## Description`, `## Key References`, `## Open Questions`.
+5. **Validate the topic file** before proceeding: run `uv run python research/atlas/schema.py topics/{theme-dir}/{slug}.md` from the atlas directory. If validation fails, fix the file before syncing to vault.
+6. Update `research/atlas/themes.md` — add slug to the correct theme's topic list. If new theme needed: add row, create directory, create vault theme entry (`data_source_id: 2e8baef4-3e2e-4ea5-b25a-18a71ed47690`).
+
+## 6b. Create vault Atlas Entry
+
+1. Look up the theme's vault file ID via `mcp__taskflow__search_tasks`
+2. Create Atlas entry via `mcp__taskflow__create_task` with parent `data_source_id: 0a227f82-60f4-451a-a163-bff2ce8fa9c3`
+3. Map YAML fields to vault properties per [`atlas-schema.md`](atlas-schema.md)
+4. Set Theme relation: `"[\"~/Research-Vault/{theme-page-id}\"]"`
+5. Only use valid Methods multi-select values (see schema reference)
+
+## 6c. Create vault Pipeline Entry
+
+1. Create Pipeline row via `mcp__taskflow__create_task` with parent `data_source_id: YOUR-PIPELINE-DATABASE-ID-HERE`
+2. Set: `Project Name` (title), Stage, Target Journal, Co-authors, Priority ("Medium")
+3. Save the returned Pipeline page ID
+4. **Link Pipeline→Atlas topic** via a separate `mcp__taskflow__update_task` call:
+   - Property name: `Topics` (NOT "Related Topics" — that's the Atlas-side name)
+   - Value format: `"Topics": "~/Research-Vault/{atlas_page_id_no_dashes}"`
+   - This is a dual relation: setting `Topics` on Pipeline also sets `Papers` on the Atlas entry
+   - **This step cannot be done during creation** — the relation must be set via `update_properties` after both pages exist
+5. Link to Venues via "Target Venue" relation (search Venues DB `YOUR-CONFERENCES-DATABASE-ID-HERE` for venue pages)
+6. **Verify the link**: fetch the Pipeline entry and confirm `Topics` contains the Atlas page URL
+7. Save the Pipeline vault file URL for the confirmation report
+
+## 6d. Create Project Folder
+
+Create the project directory under the research projects root. Detect root location:
+
+```bash
+# Dropbox (MacBook)
+if [ -d "$HOME/Library/CloudStorage/YOUR-CLOUD/Research" ]; then
+  RESEARCH_ROOT="$HOME/Library/CloudStorage/YOUR-CLOUD/Research"
+else
+  RESEARCH_ROOT="$HOME/Projects"
+fi
+mkdir -p "$RESEARCH_ROOT/{Theme Name}/{Project Name}"
+```
+
+## 6e. Regenerate RECAP.md
+
+```bash
+uv run python research/atlas/generate_recap.py
+```
+
+## 6f. Update Atlas Counts
+
+If topic or theme count changed, update `research/atlas/CLAUDE.md` topic/theme counts and theme directory listing.
+
+## Atlas Defaults
+
+| Setting | Default | Override |
+|---------|---------|---------|
+| Status | `Idea` | User specifies |
+| Priority | `Medium` | User specifies |
+| Data Availability | `None` | User specifies |
+| Feasibility | `Medium` | User specifies |
+| Institution | Infer from theme/co-author | User specifies |

package/skills/init-project-research/references/atlas-schema.md

@@ -0,0 +1,81 @@
+# Atlas Schema Reference
+
+## Vault paths
+
+| Database | Data Source ID |
+|----------|---------------|
+| Research Themes | `2e8baef4-3e2e-4ea5-b25a-18a71ed47690` |
+| Topic Inventory (Atlas) | `0a227f82-60f4-451a-a163-bff2ce8fa9c3` |
+
+## Theme → Vault Path Mapping
+
+Look up the theme page ID before creating atlas entries. Theme is a **relation** property — pass as JSON array of page URLs.
+
+To find a theme's page ID: query the Research Themes database or use `mcp__taskflow__search_tasks` for the theme name.
+
+Format for the Theme relation property:
+```
+"Theme": "[\"~/Research-Vault/<theme-page-id-no-dashes>\"]"
+```
+
+## YAML Frontmatter Template
+
+```yaml
+---
+title: "Topic Name"
+theme: "Theme Name"  # Must match a theme in themes.md
+status: "Idea"  # Idea | Exploring | Active Project | Parked | Archived
+institution: "Bath"  # Warwick | Bath | Southampton | UPF | None
+project_path: "Theme Name/Project Name"  # Relative to Projects/
+linked_projects: []
+connected_topics: ["slug-1", "slug-2"]  # kebab-case slugs of related topics
+methods: ["Game Theory", "Formal Model"]
+co_authors: "Name"
+outputs:
+  - venue: "Venue Name"
+    format: "Full paper"  # Full paper | Extended abstract | Perspective | Working paper
+    status: "Planned"  # Planned | Drafting | Submitted | Accepted | Published
+    label: ""  # Optional: short label for multi-output topics
+    deadline: ""  # Optional: YYYY-MM-DD
+feasibility: "High"  # High | Medium | Low
+data_availability: "None"  # Open Data | Exists (needs access) | Needs Collection | None
+priority: "Medium"  # Critical | High | Medium | Low
+---
+```
+
+## Body Template
+
+```markdown
+## Description
+
+[1-3 sentences: core research question and approach]
+
+## Key References
+
+- [Source: Scout report or existing paper]
+- [Scout novelty score if available]
+
+## Open Questions
+
+- [Key unknowns]
+```
+
+## Vault Methods Multi-Select Options
+
+Only these values are valid (others will error):
+`MCDM`, `Experiment`, `Formal Model`, `Survey`, `Simulation`, `Econometrics`, `Game Theory`, `Meta-Analysis`, `Qualitative`, `NLP/ML`
+
+If a topic uses methods not in this list (e.g., "Mechanism Design", "Cryptography"), map to the closest valid option or omit.
+
+## File Naming
+
+- Topic file: `kebab-case-slug.md` in `research/atlas/topics/{theme-dir}/`
+- Theme directories: `operations-research/`, `behavioural-decision-science/`, `ai-safety-governance/`, `human-ai-interaction/`, `mechanism-design/`, `nlp-computational-ai/`, `political-science/`, `organisation-strategy/`, `environmental-economics/`
+
+## Research Project Path
+
+```
+$RESEARCH_ROOT/{Theme Name}/{Project Name}/
+```
+
+Where `$RESEARCH_ROOT` is `~/Library/CloudStorage/YOUR-CLOUD/Research` (MacBook) or `~/Projects` (Mac Mini).

package/skills/init-project-research/references/confirmation-report.md

@@ -0,0 +1,39 @@
+# Phase 9: Confirmation Report Template
+
+> Print this after all phases complete in `/init-project-research`.
+
+```
+Created research project: <Working Title>
+
+Directory:  <full path>
+Structure:  <N> folders, <N> files
+Git:        initialised on branch main (<short commit hash>)
+GitHub:     <URL or "local-only">
+Overleaf:   paper/ → <target path>
+
+Atlas & Pipeline:
+  - Atlas topic file:             research/atlas/topics/{theme}/{slug}.md
+  - vault atlas entry:           created (<URL>)
+  - vault pipeline entry:        created (<URL>)
+  - Venue links:                  <venue names>
+  - Project folder:               created
+  - RECAP.md:                     regenerated
+
+Task Management updates:
+  - projects/_index.md:           added row
+  - projects/papers/<name>.md:    created
+  - current-focus.md:             updated
+
+Literature & Discovery:
+  - Literature review:            docs/literature-review/YYYY-MM-DD-initial-review.md (<N> papers)
+  - Bibliography:                 docs/literature-review/references.bib
+  - Scout novelty:                docs/YYYY-MM-DD-scout-novelty.md (score: X/10)
+  - Atlas topic updated:          key references + novelty assessment added
+
+Setup log:  log/<filename>    created
+
+Next steps:
+  1. Open Overleaf and set up main.tex
+  2. Review literature map in docs/literature-review/
+  3. Start drafting in paper/
+```

package/skills/init-project-research/references/domain-profile-template.md

@@ -0,0 +1,104 @@
+# Domain Profile Template
+
+> Copy this template to your project's `docs/domain-profile.md` and fill it in.
+> All agents and skills read this file to calibrate field-specific behaviour.
+> Adapted from Sant'Anna's clo-author domain-profile system.
+
+## Field
+
+**Primary:** [e.g., Health Economics, Labour Economics, Development, IO, Public Finance, Organisational Behaviour]
+**Adjacent subfields:** [e.g., Labour, Public, IO — fields whose methods and journals overlap]
+
+---
+
+## Target Journals (ranked by tier)
+
+<!-- Used for journal selection and literature prioritisation. -->
+
+| Tier | Journals |
+|------|----------|
+| Top-5 | AER, Econometrica, JPE, QJE, REStud |
+| Top field | [e.g., JHE, RAND JE, AEJ:EP, AEJ:Applied, Management Science] |
+| Strong field | [e.g., Health Affairs, AJHE, JPubE, JHR, Organization Science] |
+| Specialty | [e.g., Medical Care, Health Services Research, JEBO] |
+
+---
+
+## Common Data Sources
+
+<!-- Prioritised during data discovery. -->
+
+| Dataset | Type | Access | Notes |
+|---------|------|--------|-------|
+| [e.g., CPS] | [survey/admin/panel] | [public/restricted] | [key strengths and limitations] |
+
+---
+
+## Common Identification Strategies
+
+<!-- Considered first during strategy design. -->
+
+| Strategy | Typical Application | Key Assumption to Defend |
+|----------|-------------------|--------------------------|
+| [e.g., State-level DiD] | [Policy variation across states] | [Parallel trends in outcomes across treated/control states] |
+| [e.g., RDD at eligibility threshold] | [Programme eligibility cutoff] | [No manipulation of running variable at cutoff] |
+| [e.g., IV with shift-share] | [Labour supply shocks] | [Exclusion restriction: instrument affects outcome only through treatment] |
+
+---
+
+## Field Conventions
+
+<!-- Followed by estimation and writing skills. -->
+
+- [e.g., Binary outcomes → report LPM alongside logit/probit marginal effects]
+- [e.g., Cost outcomes → log transform or GLM (Gamma, log link)]
+- [e.g., Clustering at state level for state-level policy variation]
+- [e.g., Always discuss moral hazard / adverse selection implications]
+- [e.g., Welfare analysis expected in top-5 submissions]
+- [e.g., Stars: * p < 0.10, ** p < 0.05, *** p < 0.01]
+
+---
+
+## Notation Conventions
+
+<!-- Enforced in paper writing and reviewing. -->
+
+| Symbol | Meaning | Anti-pattern |
+|--------|---------|-------------|
+| [e.g., $Y_{it}$] | [Outcome for individual i at time t] | [Don't use $y$ without subscripts] |
+| [e.g., $D_{it}$] | [Treatment indicator] | [Don't use $T$ — conflicts with time] |
+| [e.g., $\beta$] | [Parameter of interest] | [Don't use $b$ for coefficients] |
+
+---
+
+## Seminal References
+
+<!-- Ensures these are cited when relevant. -->
+
+| Paper | Why It Matters |
+|-------|---------------|
+| [e.g., Finkelstein et al. (2012)] | [Oregon HIE — gold standard for insurance effects] |
+| [e.g., Callaway & Sant'Anna (2021)] | [Modern DiD with staggered treatment] |
+
+---
+
+## Field-Specific Referee Concerns
+
+<!-- Watch list for peer review simulation. -->
+
+- [e.g., "Why not use the Oregon HIE?" — must address if studying insurance effects]
+- [e.g., "Selection into treatment" — always a concern in health care utilisation studies]
+- [e.g., "External validity" — Medicaid population ≠ general population]
+- [e.g., "Moral hazard vs adverse selection" — referees expect you to distinguish]
+
+---
+
+## Quality Tolerance Thresholds
+
+<!-- Customise for your domain's standards. -->
+
+| Quantity | Tolerance | Rationale |
+|----------|-----------|-----------|
+| Point estimates | [e.g., 1e-6] | [Numerical precision] |
+| Standard errors | [e.g., 1e-4] | [MC variability] |
+| Coverage rates | [e.g., ± 0.01] | [Simulation with B reps] |