chore: remove mcp-notebook, slim down CLAUDE.md, clean up repo

.agents/skills/deus-code-style/SKILL.md

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+---
+name: deus-code-style
+description: "Deus Machine internal code style and conventions. Use when writing, reviewing, or modifying code in this project. Covers Tailwind v4, component patterns, animations, and performance. Triggers on: writing code, styling, components, CSS, tailwind, shadcn, animation, performance, database query, polling, rendering, zustand, react query."
+---
+
+# Deus Code Style
+
+Internal conventions for writing code in the Deus Machine codebase.
+
+## Quick Reference
+
+| Topic | Guide | When to use |
+|---|---|---|
+| [Tailwind & Styling](tailwind.md) | Tailwind v4 gotchas, global CSS rules, color system | Writing any CSS or styling |
+| [Components](components.md) | Shadcn, file locations, architecture patterns | Creating or modifying UI components |
+| [Animations](animations.md) | Easing defaults, CSS vs Framer Motion, performance | Adding motion or transitions |
+| [Performance](performance.md) | DB rules, polling, rendering, git subprocess | Backend queries, frontend lists, data fetching |
+
+## Core Conventions
+
+### ts-pattern for Discriminated Unions
+
+Use `ts-pattern` instead of switch/case or if/else chains on `.type`, `.status`, `.state` fields:
+
+```tsx
+import { match, P } from "ts-pattern";
+
+return match(block)
+  .with({ type: "text" }, (b) => <TextBlock block={b} />)
+  .with({ type: "tool_use" }, (b) => <ToolUseBlock block={b} />)
+  .exhaustive(); // catches missing cases at compile time
+```
+
+- `.exhaustive()` — all cases must be handled
+- `.otherwise()` — intentional fallback for open-ended matching
+
+### State Management Split
+
+- **Zustand** — UI state only (modals, selections, layout, sidebar)
+- **TanStack Query v5** — Server state (workspaces, sessions, repos, messages, settings)
+
+Feature hooks: `src/features/{feature}/api/{feature}.queries.ts` and `.service.ts`. Never put server data in Zustand.
+
+### File Organization
+
+```
+src/features/{feature}/ui/    # Feature-scoped components (default)
+src/shared/components/         # Cross-feature reusable compositions
+src/components/ui/             # Shadcn base primitives (edit freely)
+src/platform/                  # Platform abstraction (Electron IPC, socket)
+```
+
+Default to feature-scoped. Only promote to `shared/` when a second feature needs it.
+
+### Git Diff Semantics
+
+- Branch resolution always prefers **remote** (`origin/{branch}`) over local — never change to local-first
+- Diffs use git CLI against **working directory** (committed + staged + unstaged) — `diff_tree_to_tree` would miss uncommitted changes
+- All git calls use `spawn()` with timeouts (5s short ops, 15s diffs)

.agents/skills/deus-code-style/animations.md

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+# Animations
+
+## Project Defaults
+
+- **Default easing:** `ease-out-quart` — `cubic-bezier(.165, .84, .44, 1)`
+- **Default duration:** 200-300ms. Never exceed 1s.
+- **Hover transitions:** `200ms ease` for color/background/opacity. Disable on touch with `@media (hover: hover) and (pointer: fine)`.
+- **Don't use built-in CSS easings** (`ease-out`, `ease-in`) except `ease` for hover and `linear` for constant-speed. Always custom cubic-bezier.
+
+## CSS vs Framer Motion
+
+**CSS/Tailwind** for:
+- Hover/focus transitions
+- Infinite loops (spinners, shimmers)
+- Tooltip/popover enter/exit
+- Simple opacity/transform keyframes
+
+**Framer Motion** for:
+- Mount/unmount transitions (`AnimatePresence` + `initial`/`animate`/`exit`)
+- Layout animations (items shifting after reorder)
+- Staggered lists (`staggerChildren`)
+- Height auto (CSS can't animate to `auto`)
+
+## Rules
+
+- Animate only `transform` and `opacity` — never width, height, top, left, margin, padding
+- `will-change` only for: transform, opacity, clipPath, filter
+- No blur above 20px
+- Co-locate animation config with the component, not in global.css
+- Never define `@keyframes` in global.css for a single component — use Framer Motion inline
+- Reuse: `{ duration: 0.2, ease: [0.165, 0.84, 0.44, 1] }` (ease-out-quart)
+- Always wrap conditional renders in `AnimatePresence` when exit animations are needed

.agents/skills/deus-code-style/components.md

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+# Components
+
+## Shadcn — You Own the Code
+
+Files in `src/components/ui/` are starter code you're meant to customize. Editing them directly is the intended workflow.
+
+### Edit `components/ui/*` directly when:
+- Changing default styles, adding project-wide variants, fixing a11y, adjusting animations
+
+### Create feature components when:
+- Adding app-specific behavior, combining shadcn primitives into domain patterns, adding business logic
+
+### Shadcn Rules
+
+1. **Theme first** — try CSS variables in `global.css` before editing components. If you're overriding the same className everywhere, edit the component once.
+2. **Keep standard props** — preserve `className`, `variant`, `size`, `asChild`. Don't embed domain logic in `ui/*`.
+3. **Refresh from upstream** with `bunx shadcn@canary add <component> --overwrite`, then reapply customizations.
+
+## Component Architecture
+
+### Encapsulate Self-Contained Concerns
+
+If a piece of UI involves data derivation + rendering + state, make it a component. Don't scatter utilities across the parent.
+
+```tsx
+// Bad — parent wires up avatar logic manually
+function Item({ repo }) {
+  const owner = getRepoOwner(repo.name);
+  const url = getGitHubAvatarUrl(owner);
+  return <Avatar><AvatarImage src={url} />...</Avatar>;
+}
+
+// Good — component owns its concern
+function Item({ repo }) {
+  return <RepoAvatar repoName={repo.name} />;
+}
+```
+
+### Extract vs Keep Inline
+
+**Extract when:** combines data + rendering, has own state/hooks, reusable, 10+ lines distracting from parent.
+
+**Keep inline when:** pure layout div, one-liner, only makes sense in this parent.
+
+### Where Components Live
+
+| Location | What goes here |
+|---|---|
+| `src/features/{feature}/ui/` | Default. Feature-scoped components. |
+| `src/shared/components/` | Cross-feature reusable compositions (only when 2+ features need it) |
+| `src/components/ui/` | Shadcn base primitives only |

.agents/skills/deus-code-style/performance.md

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+# Performance
+
+The app manages tens of repos, hundreds of workspaces, and multiple concurrent agent sessions. Naive patterns compound at this scale.
+
+## Database
+
+- **Index every query pattern** — all indexes in `shared/schema.ts`. Add one for any new query.
+- **No N+1** — never subquery per row. Use `sessions.last_user_message_at` directly. Batch or denormalize.
+- **Paginate unbounded collections** — messages, file lists. Default 50-100 items.
+- **Auto-update triggers** for `updated_at` columns.
+- **Column deprecation** — rename with `DEPRECATED_` prefix, never drop.
+- **PRAGMA optimize** on startup and graceful shutdown.
+
+## Polling Discipline
+
+- **WebSocket push over polling** — all data resources use WS subscriptions. Never poll data that has a subscription.
+- **Budget:** <5 HTTP req/sec steady state. Only pollers: git diffs on working sessions (2-5s).
+- **Gate polling on state** — don't poll idle workspaces.
+
+| Frequency | What |
+|---|---|
+| 2-5s | Git diff hooks (only when session status = "working") |
+| 30s+ / on-demand | Settings, repos, config, PR status |
+| Never poll | Workspaces, stats, sessions, messages (WS push) |
+
+## Frontend Rendering
+
+- **Virtualize unbounded lists** — anything >30 items uses `@tanstack/react-virtual` (sidebar, messages, file tree)
+- **Zustand selector discipline** — never destructure entire store. Always individual selectors:
+  ```tsx
+  // Bad: const { x, y } = useStore();
+  // Good: const x = useStore((s) => s.x);
+  ```
+  Use `useShallow` for structurally-equal objects/arrays.
+- **Memoize list items** — `React.memo()` on components in `.map()` loops
+- **Batch queries** — use bulk endpoints (e.g. `useBulkDiffStats`), not per-item hooks
+
+## Git + Subprocess
+
+- Treat git calls as expensive — deduplicate aggressively
+- Use bulk endpoints (one call per repo interval), not per-item hooks
+- Cache diff results with short TTL (5-10s)
+- Cap concurrent git subprocesses to prevent CPU spikes
+
+## Read-Layer Priority
+
+When optimizing, tackle in this order:
+1. `GET /workspaces/by-repo` (heaviest — joins repos + workspaces + sessions)
+2. `GET /stats` (consolidated count query)
+3. `GET /sessions/:id`
+4. `GET /sessions/:id/messages` (paginated, cursor-based)
+5. On-demand reads (repos, settings, config, PR status)

.agents/skills/deus-code-style/tailwind.md

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+# Tailwind & Styling
+
+## Tailwind CSS v4 — Key Differences
+
+v4 is NOT v3. These are the traps:
+
+- **No JavaScript config.** All config lives in `src/global.css` using `@theme` directive. Never create `tailwind.config.js`.
+- **No `@layer`** — `@layer base/components/utilities` is not supported in v4.
+- **No `@apply`** — use vanilla CSS instead.
+- **No `@theme inline`** — put everything in the main `@theme` block.
+- **No `tailwindcss-animate`** — animations are built-in.
+- **Vite plugin:** `@tailwindcss/vite` (not `@tailwindcss/postcss`).
+
+### Color System: OKLCH
+
+All colors use OKLCH, not HSL/RGB. Semantic colors in `:root` and `.dark`:
+
+```css
+@theme {
+  --color-background: var(--background);
+  --color-primary: var(--primary);
+  --font-family-sans: "Helvetica Neue", -apple-system, ...;
+}
+```
+
+For semi-transparent: `color-mix(in oklch, var(--primary) 25%, transparent)`.
+
+## What Goes Where
+
+### Global CSS (`src/global.css`) — ONLY:
+
+1. `@theme` block (design tokens)
+2. `@keyframes` (GPU-accelerated animations shared across components)
+3. Global element styles (`html`, `body`, `#root`, scrollbars)
+4. Complex effects Tailwind can't do (vibrancy, backdrop filters, markdown content styling)
+5. `@media (prefers-reduced-motion)`, `@media (hover: hover)`
+
+### Never add to global CSS:
+
+Simple utilities that Tailwind already handles — spacing, shadows, typography, layout, colors. If Tailwind does it in 2-3 classes, don't make a custom utility.
+
+### Component variants (`src/components/ui/*`):
+
+Repeated patterns: size variations (`size="sm"`), style variations (`variant="outline"`), state variations (`data-state="active"`).
+
+### Inline Tailwind:
+
+Layout, one-off adjustments, responsive, state variants — the usual.
+
+## Specificity & Overrides
+
+- Never use `!important` — if you need it, the specificity architecture is wrong
+- `cn()` / twMerge only merges classes with **identical modifiers**. `has-[>svg]:px-3` and `has-[&>svg]:px-1` coexist instead of overriding. Always match the exact modifier string from the base component.
+- When debugging spacing, always read the base component source (`components/ui/*.tsx`) to see what CVA defaults you're inheriting
+
+## Debugging Layout Issues
+
+Before touching CSS:
+
+1. Outline everything: `* { outline: 1px solid rgba(255,0,0,0.3) !important; }` in DevTools
+2. Trace the full component tree (parent + element + children across files)
+3. Check parent/grandparent for `p-*`, `gap-*`, flex alignment
+4. Check compound spacing (parent padding + child margin + flex gap)
+5. Read the shadcn base component source for hidden defaults
+
+## General Rules
+
+- All colors via CSS variables/tokens, never hardcoded (`bg-blue-500`, `#3b82f6`)
+- Consistent 16px default padding (dense product)
+- Use container queries (`@container`) over media queries for reusable components
+- Prefer logical properties (`margin-inline`, `padding-block`) for future-proofing