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neuroflow Development Guide

Repo structure

neuroflow/
├── .claude-plugin/
│   ├── plugin.json        ← plugin manifest (bump version here on release)
│   └── marketplace.json   ← marketplace catalog (lists neuroflow as installable plugin)
├── .github/
│   ├── agents/
│   │   └── neuroflow-developer.md   ← GitHub/Copilot-compatible dev agent
│   └── workflows/
│       ├── deploy-docs.yml          ← builds and deploys MkDocs site on push to main
│       ├── daily-maintenance.yml    ← posts daily maintainer report (Discussion #167)
│       ├── research-radar.yml       ← posts weekly research radar (Discussion #169)
│       └── sentinel-dev.yml         ← runs sentinel consistency checks (Discussion #168)
├── scripts/
│   └── automation/                  ← Python scripts used by GitHub Actions
│       ├── sentinel_check.py
│       ├── daily_maintenance.py
│       ├── research_radar.py
│       ├── post_discussion.py
│       └── requirements.txt
├── skills/                ← agent-invoked skills (SKILL.md per folder)
├── commands/              ← slash commands (one .md file per command)
├── agents/                ← Claude Code custom agent definitions (.md files)
├── hooks/
│   └── hooks.json         ← event hooks (PostToolUse, PreToolUse, etc.)
├── docs/
│   └── commands/          ← MkDocs source pages (one .md per command)
├── overrides/             ← MkDocs theme overrides (main.html)
├── AGENTS.md              ← agent entry points for non-Claude Code tools (Codex, OpenCode)
├── mkdocs.yml             ← docs site nav, theme, plugins, extra.version
├── requirements.txt       ← Python deps for the docs build (mkdocs-material)
├── .neuroflow/            ← plugin-level project memory (dev decisions, sentinel reports)
└── README.md              ← public docs: What's new, Commands/Skills/Agents/Hooks tables

Before adding anything — overlap audit

Every proposed addition (skill, command, agent, hook) must be checked against what already exists. Do this before writing a single line:

  1. Read all existing SKILL.md files in skills/*/SKILL.md — extract the name, description, and key responsibilities of each.
  2. Read all existing command files in commands/*.md.
  3. Read all existing agent files in agents/*.md.
  4. Read hooks/hooks.json for active hooks.

Then answer these questions explicitly:

Question If YES →
Does an existing skill cover more than 50% of the proposed scope? Extend that skill instead
Does the proposed skill duplicate a command's instructions? Merge into the command or drop the skill
Does the proposed agent repeat logic already in a skill? The skill is enough — agents add autonomous execution, not knowledge
Does the proposed hook fire on the same event as an existing hook? Combine into one hook command
Is the proposed addition genuinely new territory? Proceed with adding it

Write your conclusion before proceeding. Example:

"The proposed eeg-analysis skill overlaps with the eeg-preprocessing skill (filtering, ICA) and the feature-extraction skill (band power). The unique contribution is connectivity analysis. Recommendation: extend eeg-preprocessing with a connectivity section rather than adding a new skill."

Only if the contribution is clearly new and non-overlapping should you create a new file.

Adding a new skill

  1. Create a folder under skills/ — the folder name becomes the skill name
  2. Add a SKILL.md with frontmatter and instructions:
---
name: my-skill
description: One-line description Claude uses to decide when to invoke this skill.
---

Instructions for Claude to follow when this skill is invoked...

Skills are namespaced as neuroflow:my-skill after installation.

Adding a new command

Create a .md file in commands/. The filename becomes the command name. Every command must include the standard frontmatter defined in neuroflow:neuroflow-core:

---
name: my-command
description: What this command does
phase: <phase-name>        # matches command name, or "utility" for stateless commands
reads:
  - .neuroflow/project_config.md
  - .neuroflow/flow.md
  - .neuroflow/{phase}/flow.md    # only if command has a phase subfolder
writes:
  - .neuroflow/sessions/YYYY-MM-DD.md
  - .neuroflow/{phase}/           # only if command has a phase subfolder
  - .neuroflow/{phase}/flow.md    # only if command has a phase subfolder
---

Instructions Claude follows when the user runs /neuroflow:my-command...

Valid phase values: ideation, preregistration, grant-proposal, finance, experiment, tool-build, tool-validate, data, data-preprocess, data-analyze, paper, review, notes, write-report, output, hive, brain-build, brain-optimize, brain-run, utility

Every command must also follow the lifecycle defined in neuroflow:neuroflow-core — read project_config.md + flow.md at the start, write to sessions/ and update flow.md at the end.

Project memory — .neuroflow/

Project state lives in the user's working directory, not inside the plugin. The /neuroflow command creates .neuroflow/ there by interviewing the user.

Skills, commands, and agents that need project context must explicitly Read .neuroflow/project_config.md from the working directory at runtime. It is never auto-injected.

When building a new skill/command/agent that needs project context: 1. Read neuroflow:neuroflow-core to understand the full .neuroflow/ structure 2. Declare what you read and write in the frontmatter reads / writes fields 3. Handle the case where .neuroflow/ doesn't exist — prompt the user to run /neuroflow first, or proceed with sensible defaults

There is no config folder in the plugin — project state is always per-project, in the user's repo.

Adding a new agent

Create a .md file in agents/. Define the agent's role, focus, and any tool restrictions in the body.

Adding or modifying hooks

Hooks are defined in hooks/hooks.json as shell commands triggered by tool-use events.

Every hook command MUST fail silently. Hook failures that surface to the user create noise during sessions. Enforce this by always ending hook commands with one of: - ; true — guarantees exit code 0 regardless of what preceded it - || true — falls back gracefully on any error - 2>/dev/null — suppresses all stderr output (use alongside ; true)

Use plain shell commands where possible (they are simpler and avoid Python import/quoting issues). Redirect both stdout and stderr of any tool invocation (>/dev/null 2>&1).

Example of a well-formed hook: 

# CLAUDE_TOOL_RESULT_FILE_PATH may not always be set (or the file may be gone
# by the time the hook runs), so check for .py extension AND file existence.
f="${CLAUDE_TOOL_RESULT_FILE_PATH:-}"; case "$f" in *.py) [ -f "$f" ] && ruff format "$f" >/dev/null 2>&1;; esac; true

Run sentinel-dev after changing hooks/hooks.json — Check 8b will flag any hook command that lacks error suppression.

Release workflow

  1. Make your changes
  2. If you added, renamed, or removed a command, skill, or agent: update docs/javascripts/mind.js — add (or remove) the node in NODES, the link in LINKS, the phase angle in PHASE_ANGLES (if a new phase), and the entry in NODE_PHASE_MAP. Run a quick Select-String -Pattern "sk-|cmd-|ag-" docs/javascripts/mind.js sanity check after editing.
  3. Blocking step — do not skip. Omitting a mind.js entry for a new skill, command, or agent is a consistency error that sentinel-dev Check 11 will flag on the next run.
  4. Update README.md — two places:
  5. Replace the ## What's new in X.Y.Z section with the new version number and up to 3 bullet points describing what changed. Each bullet should link to the relevant file. This is the first thing users see after the header — keep it tight.
  6. Add the new command or skill to the Commands or Skills table if applicable, with a link to the file.
  7. Add an entry to docs/changelog.md — same bullet points as the README section, formatted as ## X.Y.Z heading followed by one-line summaries.
  8. Update mkdocs.yml extra.version to match the new version.
  9. If it's a new item, add it to the Roadmap as completed or remove it from the planned list.
  10. Update the self-assessment bar in docs/index.md — change sa-bar-version to the new version, and re-run the probe honestly for this version of Claude (answers may change as the model evolves).
  11. Review commands/neuroflow.md one-liners — add, remove, or rotate the random lines printed below the ASCII logo if any feel stale for this release.
  12. Bump the patch version in all four places (always patch: 0.1.0 → 0.1.1 → 0.1.2, regardless of how large the change is):
  13. .claude-plugin/plugin.json → version field
  14. .claude-plugin/marketplace.json → plugins[].version field
  15. .neuroflow/project_config.md → Plugin version: line (the plugin's own project memory)
  16. mkdocs.yml → extra.version field (also covered by step 4 above, but keep in sync)
  17. Run sentinel-dev to verify internal consistency before committing.
  18. Commit and push to GitHub:
git add -A
git commit -m "feat: describe what changed"
git push
  1. Users update their local install:
/plugin marketplace update neuroflow

Claude Code detects updates by comparing version numbers. If the version is not bumped, the update will not be pulled even if files changed.

Local development (test before pushing)

Load the local repo directly without installing:

claude --plugin-dir ./neuroflow

Skills and commands will be available as /neuroflow:skill-name. Restart Claude Code after each change to pick up edits.

One-time hook setup (required after every fresh clone):

uv run python scripts/automation/install_hooks.py

This sets core.hooksPath = .githooks, enabling the pre-push version check. The hook rejects pushes where tracked files changed but plugin.json version was not bumped. Override with git push --no-verify if needed.

Installation (for new users)

/plugin marketplace add stanislavjiricek/neuroflow
/plugin install neuroflow@neuroflow