Manage research portfolio

Manage Research Portfolio

Use this skill as the operating guide for a research portfolio: many projects sharing one overview, one data-governance area, one cross-project AI memory, and one dashboard board. It transfers a small set of durable habits: clear folder roles, narrow record locations, a compact dashboard that is a current-state map (not a log), server-side safety, and explicit handoffs.

Two rules run through everything:

1. Markdown first, board second. Update the registry or the narrowest _ai/source note first, then sync PROJECT_DASHBOARD.html.
2. The portfolio stays compact. Detailed experiments, data dictionaries, and paper notes live inside each project; the overview only holds portfolio-level state and navigation.

And one habit that keeps the portfolio alive: a project can start from any path. When a new project appears, scaffold it from _PROJECT_TEMPLATE, add it to the registry, and sync its card onto the dashboard — so status flows up automatically. These behaviors are driven by the portfolio's guideline files (PROJECT_GUIDELINES.md, this skill); extend them by adding rules, and future actions follow. This is what makes multi-owner, multi-project management sustainable.

Use three portfolio lanes:

• Mainline — active or formally preparing projects with evidence, owner/status/next fields, and default dashboard visibility.
• Parked — future plans or possible projects that should be remembered but should not yet enter the project template, registry mainline, or dashboard default flow.
• Archived — abandoned, deprecated, or superseded projects preserved with a stop reason, evidence, and reactivation condition.

Do not turn every idea into a live project. Park early ideas cheaply; promote only when a decision, owner, concrete next action, or coordination need exists.

Start Here

1. Identify scope before editing:
   • Portfolio/team scope, dashboard, templates, global skills: <slug>-overview/
   • Cross-project AI context and handoffs: <slug>-ai/
   • Data governance, data inventory, access boundaries: <slug>-data/
   • A concrete research project: <slug>-project/<project-name>/
   • Future or possible project idea: <slug>-overview/_PROJECT_PARKING_LOT.md or a clearly marked parked section in the registry
   • Abandoned/deprecated project: <slug>-overview/_PROJECT_ARCHIVE.md or <slug>-project/_archive/, with stop reason and evidence
   • Portfolio challenge or drift: <slug>-overview/_CHALLENGE_REGISTER.md or <slug>-ai/<date>_challenge-review.md
   • After a project exists, run project-specific edits from that project root as the working directory, not from the portfolio root. Use the portfolio root / <slug>-overview only for overview, deployment, global rules, global skills, or cross-project synchronization.
2. Read the smallest useful context first: <slug>-overview/README.md for intent, the project registry, and any recent <slug>-ai/<date>_<topic>.md handoff related to the request.
3. For a concrete project, switch to that project and use the iterate-research-project skill (root PROJECT_GUIDELINES.md, _ai/project_overview.md, _ai/project_board_spec.md, then the numbered folders).
4. For complex tasks, keep task_plan.md, findings.md, and progress.md in the relevant overview or project directory.

Hard Boundaries

• Treat any private/sensitive data area as read-limited: default to high-level descriptions, manifests, and governance notes, not row-level content.
• Never write secrets, tokens, private keys, passwords, raw identifiers, or private-data excerpts into docs, skills, HTML, or handoff files.
• Do not force every project into one rigid template. A portfolio grows lightly; suggest structure only when a project needs it.
• Do not make broad cross-project edits unless asked. Prefer one global file or one project at a time.
• Before automatic structure changes, state which files/directories will change unless the user already specified the exact target.
• Before changing data-governance defaults, raw-data write locations, derived-data ownership, public boundaries, or permission boundaries, confirm scope and exceptions every time.

Folder And Record System

Use four prefixed top-level areas. <slug> is a short portfolio name so multiple portfolios never collide (the demo uses reasoning).

<portfolio>/
├── PROJECT_GUIDELINES.md      global operating rules for the whole portfolio
├── GIT_WORKFLOW.md            shared git identity + commit policy
├── <slug>-overview/           team entry: dashboard, requirements, templates, global skills, public-dashboard
├── <slug>-project/            one folder per project + a copyable _PROJECT_TEMPLATE
├── <slug>-data/               data inventory, access boundaries, governance (raw/authoritative only)
└── <slug>-ai/                 cross-project AI handoffs and durable context (<date>_<topic>.md)

Default landing places:

• Long-lived portfolio rules: <slug>-overview/README.md, PROJECT_GUIDELINES.md, data-governance notes, or global skills.
• Cross-project AI handoff: <slug>-ai/<date>_<topic>.md.
• Project objective/status/next action: the project's _ai/project_overview.md and _ai/task_plan.md.
• Project-derived data (features, trajectories, analysis-ready tables, QC intermediates, project data dictionaries): the project's own 2-Data/, not the global <slug>-data area. Keep the global data area for raw/authoritative datasets, inventory, access boundaries, and governance.

Modular collaboration language — encourage the user to name the module type instead of saying "organize this":

• "This is a document" → one topic/meeting/method/decision; project 1-Docs/ + update 1-Docs/README.md.
• "This is a small project / attempt" → one concrete experiment or route; project 0-Project/<attempt-name>/.
• "This is a note about an existing attempt" → project 0-Project/<attempt>/docs/<date>_<topic>.md; use the iterate-research-project skill.
• "This is a future project idea" → parked lane first; do not scaffold or dashboard it until promoted.
• "This project is deprecated / abandoned" → archived lane with stop reason, replacement if any, evidence, and reactivation condition.
• "This is data information" → source/version/permissions/QC/boundary; project 2-Data/DATA.md.
• "This is context to survive compression or task switching" → write the narrowest handoff: project _ai/1-Docs/attempt docs/, or <slug>-ai/<date>_<topic>.md for portfolio-wide context.
• "This is a challenge / drift / messy state" → record a challenge first; do not fix everything in one broad edit.
• If unsure, classify first, explain the landing place, then edit.

See references/portfolio-system.md for the full folder-and-record contract, registry fields, working memory, and new-project initialization.

The Portfolio Board (看板)

The portfolio board is <slug>-overview/PROJECT_DASHBOARD.html: a team-browsable current-state console, visually distinct from any single-project roadmap (control-console feel, not a single research roadmap). It is a map and navigation surface, not a file browser or execution log.

Basic elements, coordinated with the folders:

• Persistent Portfolio Overview (always visible, compact, low height): project count, dataset count, project abbreviations, dataset abbreviations. No roadmap phases and no long prose here.

• Three mutually-exclusive views below the overview:

  View	Fed by	Shows
  Project Board	<slug>-project/ + registry	one card per project: title, priority + owner tags, status, time, next action, and a link to the project's public page. Core view; the template project is pinned first.
  Data Board	<slug>-data/	a two-level classification (access boundary → data type) with actual registered datasets listed under each category, distinct from the classification dimensions themselves.
  Usage Guidelines	<slug>-overview + template	folder-structure cards that mirror the real tokens: the four top-level <slug>-* folders (big-project idea) and the six _PROJECT_TEMPLATE folders 0-Project/1-Docs/2-Data/3-Paper_Survey/4-Skills/_ai (single-project iteration), plus behavior norms split into everyday use and initialization.

• Narrow sidebar: title, version status, and only these three nav items — do not put the Portfolio Overview in the nav.

• Project focus (weaker area under the nav): owner filter + priority filter + a subtle matching-project list. Session-only UI state (resets on refresh); never persisted to team state.

• Editable team facts (priority, owner, status, next) belong in a protected server state store; HTML text is a fallback for failed reads, not the source of truth. Personal preferences (theme, sort, active tab) may live in browser local storage only.

• Version marker YYYY-MM-DD-vN with a freshness/refresh indicator; optional theme selector (small, cornered) and a feedback launcher (bottom-right).

• Mutually-exclusive view switching; long tokens wrap; no private data, secrets, or real local paths.

See references/portfolio-board.md for the full dashboard contract. A small portfolio can start with the text registry and add the dashboard once several projects need coordination.

Project Registry

Keep the registry in <slug>-overview/ (mirror a short index in <slug>-project/README.md). Represent mainline projects with: Project (folder/short name), Goal, Priority (TBD/low/medium/high), Owner (or TBD), Status (proposed/planning/preparing/active/blocked/paused/done/archived), Next action, Blocker, Evidence, Last sync. Status must have evidence; without it keep TBD, preparing, active, or needs review.

Keep parked and archived work separate:

Lane	Minimum fields	Promotion / exit rule
Parked future plan	Idea, why it matters, trigger to revisit, possible owner, evidence/source	Promote to mainline only when it has a concrete next action or coordination need
Archived/deprecated project	Stop reason, replacement/superseded-by, last evidence, what not to repeat, reactivation condition	Keep out of default dashboard unless reviewing history or reactivating

Challenge Triage

Treat portfolio challenges as records before repairs. Use this for sync drift, stale public copies, oversized dirty worktrees, data-provenance gaps, local-rule drift, orphaned handoffs, or deleted/archived artifacts that still appear active.

Default record: <slug>-overview/_CHALLENGE_REGISTER.md. Use <slug>-ai/<date>_challenge-review.md when the review is narrative or spans several projects.

Minimum fields: Challenge, Type, Evidence, Blast radius, Owner/TBD, Next action, Safety boundary, Sync level, Last reviewed. Keep evidence as public-safe relative paths or high-level descriptions. Do not paste private data, raw logs, local absolute paths, or source-domain details into the record.

After recording, choose one next action only: update a registry/dashboard field, open a project-level challenge note, create a concrete repair attempt, archive stale work, or ask the user to resolve ownership/safety. Broad automatic cleanup across many projects is a separate confirmed task.

New Project Creation

1. Confirm the operator's Git identity (git config user.name, git config user.email). If missing, ask the user to configure their own and pause until done. Identity is attribution + commit authorship, never a credential.
2. Create formal projects under <slug>-project/<project-name>/ by copying _PROJECT_TEMPLATE.
3. Minimally adapt every template file to the new project (README.md, PROJECT_GUIDELINES.md, PROJECT_BOARD.html, 1-Docs/README.md, 2-Data/DATA.md, 3-Paper_Survey/README.md, 4-Skills/PROJECT_SKILLS.md, and all _ai/ files). Use TBD for missing facts; do not invent owner, priority, status, boundary, data source, or results.
4. Initialize the public-safe page <slug>-overview/public-dashboard/projects/<project-slug>/index.html, add the project card to the dashboard and its server-state defaults, and set the card link to /projects/<project-slug>/.
5. Stage explicit paths and commit (never git add -A; never commit raw/derived data, logs, pid, cache, or secrets).

Sync Scale

Level	Trigger	Update
0	Read-only exploration, no new decision	Nothing
1	Local project work changed, or a challenge is recorded without changing active state	Project source files, _ai notes, or _CHALLENGE_REGISTER.md only
2	Project status, blocker, evidence, next action, owner, or priority changed	Project summary + portfolio registry + the dashboard Project Board card
3	Public claim, shared data rule, ownership, deployment/version, or a cross-project rule changed	Registry, dashboard, published public copy, and a cross-project handoff

Asking And Reminder Rules

• If user requests, portfolio rules, project docs, HTML display, or data boundaries conflict, stop the change and ask.
• Ask when missing information affects owner, public boundary, project status, next action, data safety, or whether to sync the dashboard.
• Ask before turning any decision into a portfolio-wide or cross-project rule; confirm scope, exceptions, and which rule files to update.
• For low-risk formatting/naming/classification, choose the conservative option and record the assumption in progress.md.
• If a challenge has multiple causes, split it into separate records instead of creating one vague mega-task.
• Before context gets long, after a meaningful step, or before switching projects, write a compact handoff in the narrowest matching Markdown file. Include current goal, completed step, key decisions, evidence paths, open questions, next action, and whether dashboard/board sync is needed.
• Keep questions short and concrete, preferably 2-3 options.

Publishing

Publish only reviewed, public-safe static files from <slug>-overview/public-dashboard/; never deploy the whole workspace, and never expose Markdown, scripts, logs, pid files, raw feedback, or private data as web pages. See references/public-sharing.md before preparing any public dashboard, repository, example, or community post.

Standard Workflow

1. Restore context from the overview README, registry, and recent handoff/progress notes.
2. State scope and affected files when the task will modify structure or shared rules.
3. Make the smallest durable update that solves the task; record discoveries in findings.md and actions/validation in progress.md.
4. If status, next action, evidence, data version, or public state changed, update the registry / dashboard / public copy per the Sync Scale.
5. End with a short handoff: files changed, current status, validation performed, next useful action, and the commit made.

References

• Read references/portfolio-system.md when creating or reorganizing portfolio folders, the registry, the template project, working-memory files, or handoffs.
• Read references/portfolio-board.md when creating, reviewing, or syncing PROJECT_DASHBOARD.html.
• Read references/public-sharing.md before preparing a public-facing board, repository, example, or community post.