Personal wiki (/flowie --wiki-*) — Karpathy-style LLM-maintained knowledge base inside your flowie repo; ingest sources, query accumulated knowledge, lint for orphans/contradictions/stale pages; every page is tagged to flowie projects; closing prompts in /notes, /ideation, /data-analyze, and /paper
New neuroflow:wiki skill — page types/frontmatter schema, ingest/query/lint/add/schema workflows, project tagging (always prompted), ideas.md and profile.md sync, fails integration for method pages, sentinel Check 12 for wiki health
/autoresearch — infinite worker-evaluator loop for any research artifact; per-phase criteria auto-loaded; live dashboard at localhost:8765; triggers via /autoresearch or any phase command + autoresearch keyword
Notes → flowie sync (/notes) — after every notes session, Claude offers to copy the formatted note to .neuroflow/flowie/notes/ for GitHub sync (default: yes); a local config.json stores per-project defaults for type, speaker, and project relation
Daily wellbeing tracking (/flowie --assess) — opt-in daily self-assessment for anxiety, energy, and happiness on a 1–10 scale (5=neutral); stored in flowie/wellbeing/; Claude prompts on any sync operation if today's entry is missing; enabled via /flowie --init or /flowie --assess
Removed broken pubmed-mcp-server — pubmed-mcp-server@1.0.0 on npm has an empty dist/index.js (TypeScript was never compiled before publishing); removed from plugin.json; PubMed search is now handled by paper-search-mcp-nodejs (the biorxiv server) which already includes search_pubmed and requires no credentials; PUBMED_EMAIL is no longer needed and has been removed from the setup wizard, skills, commands, and docs
Global device config (/setup) — credentials can now be saved once to ~/.neuroflow/integrations.json (global, all projects) or per-project; per-project takes precedence; Step 0 of the wizard asks which scope to use; per-project config still gitignored as before
Windows support — /setup, neuroflow:setup, and the e-INFRA reference now cover Windows paths (%USERPROFILE%), PowerShell env var syntax, and where gws detection throughout
Proxy model-name fix (proxy.mjs) — proxy now patches model field in every response chunk back to the original claude-* name, preventing Claude Code's "unexpected model" error when using custom LLM providers via Mode B
integrations.json gitignore in flowie — flowie agent now requires integrations.json to be gitignored in the flowie sync repo; warns before any push if it is missing; added to plugin .gitignore as well
New neuroflow:setup skill — agent-facing knowledge for all neuroflow integrations (PubMed, Miro, Google Workspace, custom LLM providers); mirrors the /setup wizard logic so agents can guide credential setup without running the command
New e-INFRA CC integration — einfra-cc reference documents the Czech e-INFRA CZ free LLM API for Claude Code; covers direct mode, proxy mode (with proxy.mjs script), available models table, and full terminal workflow; available to Czech academic researchers via Metacentrum membership only
/setup Step 5 — new optional custom LLM provider wizard; saves non-secret settings to integrations.json and optionally to the linked flowie profile for cross-machine sync; e-INFRA is documented as the Czech-specific example
Sequential search pipeline — the scholar agent now searches PubMed first, then bioRxiv, then fallbacks one at a time; was previously firing all sources simultaneously; reduces API contention and makes individual source failures easier to diagnose
Batch-2 downloads — paper downloads are now processed in batches of 2 rather than all at once; limits concurrent network requests and improves reliability on slow or rate-limited connections
Ideation workflow note — /ideation command and neuroflow:phase-ideation skill now document the sequential search approach in their workflow guidance
Personal research OS — flowie upgraded from identity layer to full cross-project personal OS: private GitHub repo now holds a Kanban task board (tasks/) and a project registry (projects/) alongside the existing profile.md and ideas.md
Kanban board — /flowie --tasks renders an ASCII Kanban view; --tasks --add runs a mini interview (title → project suggestion from registry → phase, due); --tasks --move, --tasks --done, --tasks --archive for column management; 7 configurable columns in tasks/config.json
Project registry — /flowie --projects lists all registered projects with ASCII phase timelines; --projects --add registers a new project with description and GitHub repo list; stored in projects/projects.json + per-project projects/{name}.md
Phase auto-sync — whenever /phase switches the active phase, if the project has a flowie_project binding it silently updates projects.json + {name}.md in the flowie repo and pushes
Auto-sync hook — any write to .neuroflow/flowie/** triggers git add -A && commit && push silently (PostToolUse hook)
Path rename — local path changed from .neuroflow/.flowie/ to .neuroflow/flowie/; flowie_profile: field in project_config.md renamed to flowie_project:
Sentinel checks — sentinel gains Check 11 (flowie structure validation); sentinel-dev gains Check 12 (stale path / field name scan)
Session logging overhaul — removed the noisy [tool] PostToolUse hook; Claude now owns all session logging and writes entries broadly after most actions; neuroflow-core logging rules are marked MUST and non-negotiable; flow.md purity rule added (pure index table only, no narrative content)
mind.js consistency check — sentinel-dev Check 11 audits that every skill, command, and agent has a node in mind.js; missing humanizer node added; neuroflow-develop release workflow now marks the mind.js update step as blocking
Grant-proposal overhaul — interview-first workflow (10-question conversational interview, objectives saved to .neuroflow/objectives.md); inspiration map from previous grants (cross-reference table saved to .neuroflow/grant-proposal/inspiration-map-[date].md); optional panel research (WebFetch + WebSearch, panel profiles saved to .neuroflow/grant-proposal/panels/); objectives tracked as cornerstones throughout the session; sequentialthinking MCP invoked before Innovation and Approach sections
Humanizer replaces stop-slop — new neuroflow:humanizer skill: AI word blacklist, structural pattern removal, rhythm checks, register calibration, voice preservation; applied across /grant-proposal, /paper, /poster, /write-report; stop-slop skill removed
Memory quality improvements — sessions use ## milestone headers (commands) + - HH:MM [tool] audit lines (hook); reasoning mandate raised to 3–5 decisions/session with mandatory trigger list; objectives.md added as a root file read at the start of every command; @modelcontextprotocol/server-sequential-thinking MCP server added; review output moved from reviews/ to .neuroflow/review/
/poster — generate a LaTeX conference poster from project memory; five templates (A0/A1 portrait, A0 landscape, 90×120 cm, 48×36 in); QR code via qrcode package; iterative poster-critic review loop (up to 3 cycles) before .tex is saved
New poster-critic agent — five-area poster auditor (content, layout, scientific communication, QR code, LaTeX correctness); returns [STATUS: APPROVED]/[STATUS: REJECTED] with specific fixes; never rewrites content
New neuroflow:phase-poster skill — full LaTeX template catalogue, template selection guide, content extraction from .neuroflow/, QR code blocks, compilation instructions
Sentinel Check 3b — sentinel now validates that .claude-plugin/marketplace.json version matches plugin.json; marketplace version was silently stuck at 0.1.0
Hardened release checklist — both dev agents now require docs/changelog.md entry, one-liner review, and marketplace.json bump on every release; neuroflow-develop/SKILL.md synced to match neuroflow-developer.md (was missing mkdocs.yml and sentinel-dev steps)
Internal consistency fixes — dead neuroflow:scholar ref in phase-paper fixed; /hive docs page created; neuroflow-developer.md and orchestrator synced to full repo structure (22 phases, all 4 workflows)
Version bump — website and header badge updated to v0.1.6
Mind map back button — the back-to-docs link on the mind map page is now a full-width prominent button, easy to spot and reach
Fails-folder awareness in core — neuroflow:neuroflow-core now instructs every command to read .neuroflow/fails/ at start (if it exists), so past logged dissatisfaction is always in context
Removed AI-slop feature claims — the "Built-in stats auditing" feature card removed from the homepage; the /data-analyze command page and skill are unchanged
/git — context-aware git utility with smart shorthand aliases (p, pl, ps, a, c, ac, acp, b, pr); reads repo state to decide push vs pull, suggests commit messages, and can open PRs via gh CLI; new neuroflow:phase-git skill
/export — export project memory or the whole project as a zip archive or folder copy; always excludes sessions and credentials; logs each export run to .neuroflow/export/; new neuroflow:phase-export skill
/preregistration — draft OSF, AsPredicted, or registered-report pre-registrations; review for completeness; log deviations; link registered reports; new neuroflow:phase-preregistration skill
/finance — budget planning, expense logging, funder-facing financial reports, and grant compliance checks; new neuroflow:phase-finance skill
/pipeline — define and run a multi-step research pipeline across any sequence of neuroflow phases; interactive by default (pauses for approval between steps), or pass --executor for brutal mode; supports resuming from a saved plan; new neuroflow:phase-pipeline skill
/search — lightweight scoped search using memory: (searches .neuroflow/) or project: (searches the codebase); uses flow.md as a fast index; read-only; new neuroflow:phase-search skill
Slash command availability in all skills — when any phase skill is invoked directly without its slash command, it now runs the full workflow and mentions the corresponding /neuroflow:<command> at the end; behavior defined in neuroflow:neuroflow-core
15 phase agents — ideation, grant-proposal, experiment, tool-build, tool-validate, data, data-preprocess, data-analyze, paper-write, paper-review, notes, write-report, brain-build, brain-optimize, brain-run — each agent is a specialist autonomous subprocess scoped to its phase, with a plan-first / confirm-before-executing discipline
neuroflow:neuroflow-core — added Default agent behavior section: scientific honesty (no sugar-coating), dry English humor, and conservative-by-default mode
/neuroflow greeting — on start, neuroflow greets with Hi, neuroflow here (v0.1.5) followed by a randomly chosen line
Behavioral flags — three prompt-level personality modes added to neuroflow:neuroflow-core: executor (aggressive evaluation loop — reruns and self-critiques until high-quality threshold is met), teacher (clarify-first mode — asks targeted questions before each step, proceeds incrementally), and critic (interrogates assumptions, surfaces hard questions first)
/quiz — neuroscience quiz command with three modes: flashcards (saveable A4 printable layout), pub quiz (with neuroscience-themed house rules), and rapid-fire throw questions (default)
/fails — log dissatisfaction (core behavior, science quality, or interaction UX) to .neuroflow/fails/, with optional one-click GitHub issue reporting; new neuroflow:phase-fails skill
/idk — personal support companion for when you're burned out, overwhelmed, or need to think out loud; breaks down impossible task lists and lets you decompress mid-research
/interview — interview preparation from either side of the table; generates tailored questions grounded in your research context, runs practice Q&A, and optionally evaluates readiness
Brain simulation commands — /brain-build, /brain-optimize, and /brain-run for assembling, fitting, and running computational brain models (NEURON, Brian2, NetPyNE, NEST, tvb-library); three new phase skills: neuroflow:phase-brain-build, neuroflow:phase-brain-optimize, neuroflow:phase-brain-run
neuroflow:phase-quiz — phase skill for /quiz covering mode behaviour, question quality standards, and mode-specific workflow
/start renamed to /neuroflow — the main entry point is now /neuroflow (run as /neuroflow:neuroflow); all command references and documentation updated
Behavioral improvements — end-of-command lifecycle hardened based on real-session feedback: continuous session logging at each milestone, live flow.md updates on every file write, phase transition prompts when outputs outpace the active phase, utility scripts routed to .neuroflow/{phase}/tools/ instead of the project root, explicit .claude/CLAUDE.md creation in the project root, decisions.md removed from scaffold (superseded by reasoning/general.json), .neuroflow/ now explicitly restricted to workflow state only
12 phase skills — neuroflow:phase-ideation through neuroflow:phase-write-report, each loaded automatically by its corresponding command to orient agent approach, relevant skills, and workflow hints
Full research pipeline — 15 commands from /neuroflow through /paper-review, each writing to .neuroflow/ project memory
neuroflow:neuroflow-core — shared lifecycle and .neuroflow/ folder spec that every command and agent follows; commands now automatically append significant decisions to .neuroflow/reasoning/{phase}.json
scholar, sentinel, sentinel-dev agents
sentinel checks plugin version against project_config.md and flags when the plugin has been updated; both sentinels clear their report to "All clear" after fixing issues
project_config.md now tracks plugin_version — kept in sync with plugin.json by /neuroflow and /sentinel
MCP servers declared in plugin.json: PubMed, bioRxiv, Miro, Context7