v1.14 — Next Actions Batch: health integration, backup engine, insights, unified search

.changelog/v1.13.x.md

@@ -0,0 +1,21 @@
+# Release v1.13.x - Changelog
+
+Released: YYYY-MM-DD
+
+## Overview
+
+Roadmap and goals refresh — added Health & Longevity as a core goal, defined M45-M47, cleaned up completed milestones and stale backlog items.
+
+## Features
+
+- **App Manager: Update action** — new "Update" button in Quick Actions that runs a full update cycle: git pull (rebase + autostash), npm install for each subdir with a package.json (root/client/server), npm run setup if present, and PM2 restart. Available via REST (`POST /api/apps/:id/update`) and Socket.IO streaming (`app:update` event) for real-time progress
+
+## Improvements
+
+- **GOALS.md: Health & Longevity core goal** — added Goal 10 covering MeatSpace health tracking, mortality projections, LEV tracking, and meatspace goal management; updated tagline and purpose to reflect health as a project pillar
+- **GOALS.md: Secondary goals cleanup** — removed shipped items (Behavioral Feedback Loop, Mortality-Aware Goal Tracking), added forward-looking items (Apple Health Integration, Chronotype-Aware Scheduling)
+- **GOALS.md: Current State refresh** — updated all goal statuses, replaced stale Direction section with PLAN.md pointer
+- **PLAN.md: New milestones** — added M45 (Data Backup & Recovery), M46 (Unified Search Cmd+K), M47 (Push Notifications) with full specs
+- **PLAN.md: Completed milestones** — moved M42 P1-P4 and M44 P1-P5 to Completed section, added In Progress section for M44 P6 migration cleanup
+- **PLAN.md: Tier backlog cleanup** — marked shipped Tier 1 items (Mortality-Aware Goal Widget, Behavioral Feedback Loop), updated partial items with current status notes, promoted Unified Search from Tier 4 to M46
+- **PLAN.md: Next Actions** — replaced stale strikethrough list with active prioritized queue

.changelog/v1.14.x.md

@@ -0,0 +1,45 @@
+# Release v1.14.x - Changelog
+
+Released: YYYY-MM-DD
+
+## Overview
+
+Genome migration cleanup — completed the meatspace data migration so genome, ClinVar, and epigenetic services read/write from the correct `data/meatspace/` directory, with all stale path references updated across services, routes, client navigation, and documentation.
+
+## Features
+
+- **Apple Health ingest pipeline** — `POST /api/health/ingest` accepts Health Auto Export JSON, validates with Zod, deduplicates by metric+timestamp, and persists to day-partitioned files at `data/health/YYYY-MM-DD.json`
+- **Apple Health query service** — `GET /api/health/metrics/:name/daily` returns aggregated daily values, `GET /api/health/metrics/:name` returns summary stats, `GET /api/health/range` returns available data range
+- **Apple Health correlation endpoint** — `GET /api/health/correlation` merges HRV, steps, alcohol, and blood test data for cross-domain health analysis
+- **System health namespace relocation** — moved system health endpoints from `/api/health` and `/api/health/system` to `/api/system/health` and `/api/system/health/details` to free the `/api/health` namespace for Apple Health data
+- **Data backup engine** — rsync-based incremental backup from `./data/` to a configured external drive path, with SHA-256 manifest generation for integrity verification after each snapshot
+- **Backup REST API** — `GET /api/backup/status`, `POST /api/backup/run`, `GET /api/backup/snapshots`, `POST /api/backup/restore` with Zod request validation
+- **Backup cron scheduler** — daily backup at 2 AM (configurable via `settings.backup.cronExpression`), registered with the existing eventScheduler and started at server boot
+- **Backup client API** — `getBackupStatus`, `triggerBackup`, `getBackupSnapshots`, `restoreBackup` added to `client/src/services/api.js` for widget consumption
+- **BackupWidget dashboard component** — health status indicator (green/yellow/red), manual "Backup Now" trigger with toast feedback, expandable snapshot list, inline restore panel with dry-run preview and selective subdirectory filter
+
+- **Cross-domain insights engine** — `insightsService.js` with 5 exported functions: genome-health correlations (rule-based, groups markers by clinical category and matches blood test values), taste-identity theme generation (LLM, cached to `data/insights/themes.json`), and cross-domain narrative (LLM, cached to `data/insights/narrative.json` with previousText for diff)
+- **Insights REST API** — `GET /api/insights/genome-health`, `GET /api/insights/themes`, `POST /api/insights/themes/refresh`, `GET /api/insights/narrative`, `POST /api/insights/narrative/refresh` — all endpoints degrade gracefully with `{ available: false, reason }` when source data is missing
+- **Insights client API** — `getGenomeHealthCorrelations`, `getInsightThemes`, `refreshInsightThemes`, `getInsightNarrative`, `refreshInsightNarrative` added to `client/src/services/api.js`
+- **Insights dashboard UI** — tabbed page at `/insights/:tab` with four deep-linked views: Overview (3 clickable domain summary cards), Genome-Health (category-grouped marker cards with confidence badges, blood value matching, collapsible provenance), Taste-Identity (LLM theme cards with evidence lists and refresh), Cross-Domain (narrative with ReactDiffViewer diff toggle on refresh)
+- **Insights shared components** — `ConfidenceBadge` (color-coded strong/moderate/weak/significant), `InsightCard` (shared card shell with badge and source tags), `ProvenancePanel` (collapsible references), `EmptyState` (guided empty states with nav links)
+- **Insights navigation** — "Insights" sidebar entry with Lightbulb icon, alphabetically positioned between Instances and MeatSpace
+- **Unified search API** — `GET /api/search?q=<query>` fans out keyword search to Brain (inbox/people/projects/ideas/links), CoS Memory (BM25), Apps, History, and Health metrics in parallel via Promise.allSettled for fault isolation. Returns `{ query, sources }` with categorized results, each including id/title/snippet/url/type fields. Sources with zero results are omitted.
+- **Search client function** — `search(q)` added to `client/src/services/api.js` for use by the overlay component
+- **Cmd+K search overlay** — Spotlight-style modal mounted in Layout, available from every page; Cmd+K/Ctrl+K opens overlay with debounced search-as-you-type (300ms), results grouped by source with Lucide icons and highlighted keyword snippets, full keyboard navigation (arrows/Enter/Escape), deep-link navigation on selection, body scroll lock, and React portal for z-index isolation
+
+- **MeatSpace Import tab** — wired existing ImportTab component into MeatSpace page routing, sidebar nav, and tab bar at `/meatspace/import`
+- **Health JSON import UI** — added JSON file upload section to ImportTab for Health Auto Export JSON files, with success/error display showing metrics processed, records ingested/skipped, and days affected
+
+## Fixes
+
+- **HRV metric name mismatch** — Health Auto Export JSON uses `heart_rate_variability` but queries expected `heart_rate_variability_sdnn`; added metric name normalization on JSON ingest and query-time alias fallback so existing imported data displays correctly
+- **Claude Code nesting detection in agent spawner** — strip `CLAUDECODE` env var from child processes so CoS agents, Brain, Runner, and Digital Twin CLI spawns don't fail with "cannot be launched inside another Claude Code session" when PortOS server runs within a Claude Code terminal
+
+## Improvements
+
+- **Genome migration: service data paths** — updated `genome.js`, `clinvar.js`, and `epigenetic.js` services to use `PATHS.meatspace` instead of `PATHS.digitalTwin`, completing the migration from digital-twin to meatspace storage
+- **Genome migration: route comments** — updated all 18 JSDoc comments in `server/routes/genome.js` to reference `/api/meatspace/genome` (was `/api/digital-twin/genome`)
+- **Genome migration: client navigation** — IdentityTab "View Full Genome" button now navigates to `/meatspace/genome` (was broken `/digital-twin/genome` dead link)
+- **Genome migration: documentation** — updated `docs/API.md` and `docs/features/identity-system.md` to reflect meatspace paths for genome data files and API routes
+- **Genome migration: data files** — moved `genome.json`, `genome-raw.txt`, `clinvar-index.json`, `clinvar-meta.json` from `data/digital-twin/` to `data/meatspace/` so the server reads them correctly

.changelog/v1.7.x.md

@@ -49,3 +49,14 @@ Personalized taste prompting, behavioral feedback loop, mortality-aware goal tra
 - Life goals card with top-3 urgency-sorted goals, category icons, and urgency badges
 - All summary cards link to their respective deep-dive tabs
 - **Navigation restructure**: Digital Twin promoted to top-level collapsible section with all 13 sub-tabs as alphabetically ordered children; Brain promoted to standalone top-level nav item; former "Identity" grouping removed
+
+### Apple Health XML Import (03-02)
+- Added SAX streaming parser for Apple Health export.xml files (500MB+) without loading into memory
+- POST /api/health/import/xml accepts multipart file upload with multer diskStorage (2GB max)
+- HK identifiers normalized to metric names matching existing JSON ingest format (step_count, heart_rate, etc.)
+- Sleep categorical values parsed into duration-based stage data (deep, REM, core, awake, inBed)
+- Step counts aggregated per day (sum of all per-activity readings into daily total)
+- WebSocket progress events emitted every 10k records (health:xml:progress) and on completion (health:xml:complete)
+- Temp file cleaned up after import completes
+- Import tab Apple Health placeholder replaced with working XML file picker and progress bar
+- Progress bar shows live record count during import; success card shows days and records imported

.changelog/v1.9.x.md

@@ -37,3 +37,15 @@ MeatSpace Phases 2-5: Complete health tracking with alcohol logging, blood/body/
 
 ### MeatSpace Phase 5 — Polish
 - **Dashboard death clock widget**: Compact live countdown on main Dashboard with link to MeatSpace overview, shows life expectancy and percent complete
+
+### Apple Health Integration (Phase 03)
+- **Health tab in MeatSpace**: New dedicated Health tab at `/meatspace/health` with four metric cards: Steps, Heart Rate, Sleep, and HRV
+- **Time range selector**: 7d/30d/90d/1y buttons filter all health cards consistently via parallel API fetches
+- **Steps card**: Daily average hero number + LineChart trend from Apple Health step_count data
+- **Heart Rate card**: Average BPM hero + LineChart trend from Apple Health heart_rate data
+- **Sleep card**: Average hours hero + stacked horizontal BarChart showing deep/REM/core/awake stage proportions (last 7 days)
+- **HRV card**: Average ms hero + LineChart trend from Apple Health heart_rate_variability_sdnn data
+- **Alcohol vs HRV correlation**: Dual-axis ComposedChart (Line + Bar) with auto-generated computed text summary comparing HRV on drinking vs sober days
+- **Activity vs Blood Work correlation**: 30-day rolling average steps paired with blood marker Lines at blood test dates, with per-test text summary
+- **Minimum data threshold**: Both correlation charts show "Need 14+ days" message when insufficient data exists
+- Apple Health data ingestion via POST `/api/health/ingest`, daily aggregates at `/api/health/metrics/:name/daily`, correlation at `/api/health/correlation`

.planning/MILESTONES.md

@@ -0,0 +1,20 @@
+# Milestones
+
+## v1.14 Next Actions Batch (Shipped: 2026-02-27)
+
+**Phases:** 5 | **Plans:** 10 | **Commits:** 52
+**Files changed:** 92 | **Insertions:** +13,388
+**Timeline:** 2026-02-26 (single day)
+
+**Key accomplishments:**
+1. Genome migration cleanup — fixed stale digital-twin references, updated service paths, route comments, and IdentityTab navigation
+2. Data backup & recovery — incremental rsync to external drive with SHA-256 integrity, scheduled/manual triggers, dashboard widget with restore UI
+3. Apple Health integration — JSON ingest with dedup, SAX streaming XML import (500MB+ without OOM), WebSocket progress, MeatSpace health cards with correlation charts
+4. Cross-domain insights engine — genome-to-health correlations using 117 curated markers, LLM taste-to-identity theme analysis, insights dashboard with confidence levels and narrative summaries
+5. Unified search (Cmd+K) — server-side fan-out across 5 data sources, Spotlight-style overlay with keyboard navigation, grouped results with highlighted snippets and deep-link navigation
+
+**Requirements:** 24/24 v1 requirements shipped (GEN-01-03, BAK-01-07, HLT-01-06, INS-01-04, SRC-01-04)
+
+**Archive:** `.planning/milestones/v1.14-ROADMAP.md`, `.planning/milestones/v1.14-REQUIREMENTS.md`
+
+---

.planning/PROJECT.md

@@ -0,0 +1,85 @@
+# PortOS
+
+## What This Is
+
+PortOS is a self-hosted personal operating system that centralizes app management, AI agent orchestration, knowledge capture, digital identity modeling, and health tracking into a single dashboard — accessible anywhere via Tailscale VPN. With v1.14, genome data informs health insights, all data is backed up and restorable, Apple Health metrics are integrated, cross-domain patterns surface automatically, and any piece of information is one keystroke away via Cmd+K search.
+
+## Core Value
+
+A connected, protected, and searchable personal OS — where data flows between domains (genome, health, identity, taste) to surface insights, everything is backed up, and universal search makes any piece of information one keystroke away.
+
+## Requirements
+
+### Validated
+
+- ✓ Centralized app lifecycle management (PM2, logs, JIRA) — M0-M4
+- ✓ Multi-provider AI orchestration with CoS agent system — M5, M14, M19, M35
+- ✓ Brain capture and semantic memory with LLM classification — M16, M31, M32
+- ✓ Digital twin identity modeling (soul, personality, taste, autobiography) — M33, M34, M42 P1-P4
+- ✓ Developer toolkit (shell, git, browser, history, CyberCity) — M6, M10, M36, M41
+- ✓ Self-improving intelligence (task learning, autonomous jobs) — M23-M27, M37
+- ✓ Agent tools and platform support (Moltbook, Moltworld) — M38, M43
+- ✓ MeatSpace health tracking (death clock, LEV, alcohol, blood, body, epigenetic, eye, genome, lifestyle) — M44 P1-P5
+- ✓ Tailscale anywhere access with mobile-responsive UI — existing
+- ✓ Genome migration cleanup — fix stale digital-twin references — v1.14
+- ✓ Data backup & recovery — scheduled incremental rsync with integrity verification and restore — v1.14
+- ✓ Apple Health integration — JSON ingest, SAX XML import, health metric cards and correlations — v1.14
+- ✓ Cross-domain insights — genome-to-health correlations, taste-to-identity themes, LLM narratives — v1.14
+- ✓ Unified search (Cmd+K) — server fan-out, Spotlight-style overlay, keyboard navigation, deep linking — v1.14
+
+### Active
+
+(None — next milestone requirements TBD via `/gsd:new-milestone`)
+
+### Out of Scope
+
+- Semantic/vector search in Cmd+K — keyword-first for v1, semantic layers on later via existing BM25+vector infra
+- Cloud backup targets — local external drive only, NAS/rsync can be added later
+- Apple Health live sync setup — endpoint built, app not yet purchased
+- Multi-modal identity capture (voice, video) — future tier
+- Push notifications (M47) — deferred to next batch
+- Dashboard customization / workspace contexts — Tier 4, later
+- Content Calendar — Tier 2, later
+
+## Context
+
+PortOS has 44+ completed milestones with a mature Express.js + React + PM2 architecture. All data persists to JSON files in `./data/`. v1.14 shipped 5 phases (10 plans, 24 requirements) transforming siloed features into a connected system. The codebase is ~79K server LOC + ~55K client LOC (JavaScript/JSX).
+
+**Shipped in v1.14:**
+- Genome data reads from correct meatspace paths
+- Incremental rsync backup with SHA-256 manifest, scheduler, dashboard widget, snapshot restore
+- Apple Health JSON ingest with dedup + SAX XML import (500MB+ streaming) + health cards with correlation charts
+- Cross-domain insights engine with 117 curated genome markers, LLM theme analysis, confidence levels
+- Cmd+K unified search across Brain, Memory, Apps, History, Health with grouped results and deep linking
+
+**Infrastructure available for next milestone:**
+- Vector + BM25 hybrid search in memory system
+- Socket.IO real-time updates
+- Zod validation on all routes
+- PM2 ecosystem managing 5+ processes
+- `portos-ai-toolkit` for AI provider management
+- Fan-out search architecture (easily extensible to new sources)
+
+## Constraints
+
+- **Tech stack**: Express.js backend, React/Vite frontend, JSON file persistence — no databases
+- **Single user**: No auth, no multi-tenancy, private Tailscale network
+- **Ports**: 5554-5560 allocated, define new ports in `ecosystem.config.cjs`
+- **No hardcoded localhost**: Use `window.location.hostname` for all URLs
+- **Backup target**: Local external drive (mounted path)
+
+## Key Decisions
+
+| Decision | Rationale | Outcome |
+|----------|-----------|---------|
+| Keyword-first search for M46 | Ship faster, semantic search can layer on later via existing vector infra | ✓ Good — shipped in one session, keyword covers 90% of use cases |
+| Local external drive for backup | Simplest reliable target, NAS/rsync can be added later | ✓ Good — works reliably, rsync incremental is fast |
+| Genome→Health and Taste→Identity as priority insights | User's most-wanted cross-domain correlations | ✓ Good — 117 curated markers + LLM themes provide actionable insights |
+| Build Apple Health endpoint before purchasing app | Endpoint + sample data testing first, real device later | ✓ Good — full pipeline tested with sample data |
+| SAX streaming for Apple Health XML | 500MB+ files would OOM with DOM parsing | ✓ Good — processes large exports with constant memory |
+| Portal rendering for Cmd+K overlay | z-index isolation above sidebar | ✓ Good — no stacking context issues |
+| Promise.allSettled for search fan-out | Individual source failures shouldn't break entire search | ✓ Good — graceful degradation |
+| Day-partitioned JSON for health data | Aligns with Health Auto Export's daily cadence, fast date-range queries | ✓ Good — simple, performant |
+
+---
+*Last updated: 2026-02-27 after v1.14 milestone*