# Nucleic session export

## Session
- **Title:** Explore Repository Contents
- **ID:** 5C9CD482-73AC-4470-B3E1-F336DD8F4D38
- **Status:** Awaiting input
- **Backend:** claudeCode
- **Backend session id:** c29d82c3-3baa-4f88-b8d1-04151486ebe4
- **Model:** claude-sonnet-4-6
- **Effort:** low
- **Branch:** main
- **Worktree:** /Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic
- **Base SHA:** —
- **Last seq:** 66
- **Transcript path:** /Users/blakeslee/Library/Application Support/Nucleic/sessions/5C9CD482-73AC-4470-B3E1-F336DD8F4D38/transcript.jsonl
- **Created:** 2026-06-12T23:13:03Z
- **Updated:** 2026-06-12T23:34:45Z

## Project
- **Name:** nucleic
- **Root:** /Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic
- **Default branch:** main

## Conversation

`#1` **User:** what's in this repo?

`#2` **session started** — model claude-sonnet-4-6

`#3` _rate limit five_hour allowed_

`#5` **Tool** `Agent` — {"description":"Quick repo overview","prompt":"Give me a concise overview of the repo at /Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic. What is it, what are the main components/directories, and what tech stack does it use? Report in under 300 words.","subagent_type":"Explore"}

`#6` `raw[system/task_started]` {"description":"Quick repo overview","prompt":"Give me a concise overview of the repo at /Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic. What is it, what are the main components/directories, and what tech stack does it use? Report in under 300 words.","session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subagent_type":"Explore","subtype":"task_started","task_id":"aa9eeac5fb94c0be0","task_type":"local_agent","tool_use_id":"toolu_01NeoJ35pHxaSHSepcpuJCLh","type":"sy

`#7` `raw[user]` {"text":"Give me a concise overview of the repo at /Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic. What is it, what are the main components/directories, and what tech stack does it use? Report in under 300 words.","type":"text"}

`#8` `raw[system/task_progress]` {"description":"Running ls -la /Users/blakeslee/Library/Mobile\\ Documents…","last_tool_name":"Bash","session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subagent_type":"Explore","subtype":"task_progress","task_id":"aa9eeac5fb94c0be0","tool_use_id":"toolu_01NeoJ35pHxaSHSepcpuJCLh","type":"system","usage":{"duration_ms":1111,"tool_uses":1,"total_tokens":9599},"uuid":"e9ebd280-786c-4f4b-9598-553947248190"}

`#10` **Tool** `Bash` — {"command":"ls -la /Users/blakeslee/Library/Mobile\\ Documents/com~apple~CloudDocs/projects/nucleic"}

`#11` **Result**: "total 80\ndrwxr-xr-x@ 17 blakeslee  staff    544 Jun 12 16:12 .\ndrwx------  35 blakeslee  staff   1120 Jun 12 16:12 ..\n-rw-r--r--@  1 blakeslee  staff   6148 Jun 11 23:49 .DS_Store\ndrwxr-xr-x@ 14 blakeslee  staff    448 Jun 12 16:11 .build\ndrwxr-xr-x@  3 blakeslee  staff     96 Jun 12 16:12 .claude\ndrwxr-xr-x@  2 blakeslee  staff     64 Jun 11 21:12 .conductor\ndrwxr-xr-x  15 blakeslee  staff    480 Jun 12 16:11 .git\n-rw-r--r--@  1 blakeslee  staff     46 Jun 12 01:13 .gitignore\n-rw-r--r--@  1 blakeslee  staff      0 Jun 11 21:12 .gitkeep\ndrwxr-xr-x   4 blakeslee  staff    128 Jun 12 02:26 .swiftpm\n-rw-r--r--@  1 blakeslee  staff  19088 Jun 12 01:13 PLAN.md\n-rw-r--r--@  1 blakeslee  staff    388 Jun 12 01:13 Package.resolved\n-rw-r--r--@  1 blakeslee  staff   1075 Jun 12 01:33 Package.swift\ndrwxr-xr-x@  6 blakeslee  staff    192 Jun 12 15:57 Sources\ndrwxr-xr-x@  3 blakeslee  staff     96 Jun 12 15:53 Tests\ndrwxr-xr-x@ 11 blakeslee  staff    352 Jun 12 01:18 docs\ndrwxr-xr-x@  3 blakeslee  staff     96 Jun 12 01:18 fixtures"

`#12` `raw[system/task_progress]` {"description":"Reading Package.swift","last_tool_name":"Read","session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subagent_type":"Explore","subtype":"task_progress","task_id":"aa9eeac5fb94c0be0","tool_use_id":"toolu_01NeoJ35pHxaSHSepcpuJCLh","type":"system","usage":{"duration_ms":4407,"tool_uses":2,"total_tokens":10381},"uuid":"d4616714-9131-421d-9fcb-4898a7cf555e"}

`#14` **Tool** `Read` — {"file_path":"/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Package.swift"}

`#15` **Result**: "1\t// swift-tools-version: 6.0\n2\timport PackageDescription\n3\t\n4\tlet package = Package(\n5\t    name: \"Nucleic\",\n6\t    platforms: [.macOS(.v14)],\n7\t    products: [\n8\t        .library(name: \"NucleicCore\", targets: [\"NucleicCore\"]),\n9\t        .executable(name: \"NucleicApp\", targets: [\"NucleicApp\"]),\n10\t        .executable(name: \"nucleic-spike\", targets: [\"nucleic-spike\"]),\n11\t        .executable(name: \"fake-claude\", targets: [\"fake-claude\"]),\n12\t    ],\n13\t    dependencies: [\n14\t        .package(url: \"https://github.com/groue/GRDB.swift.git\", from: \"7.0.0\"),\n15\t    ],\n16\t    targets: [\n17\t        .target(\n18\t            name: \"NucleicCore\",\n19\t            dependencies: [.product(name: \"GRDB\", package: \"GRDB.swift\")]),\n20\t        .executableTarget(name: \"NucleicApp\", dependencies: [\"NucleicCore\"]),\n21\t        .executableTarget(name: \"nucleic-spike\", dependencies: [\"NucleicCore\"]),\n22\t        .executableTarget(name: \"fake-claude\", dependencies: [\"NucleicCore\"]),\n23\t        .testTarget(\n24\t            name: \"NucleicCoreTests\",\n25\t            dependencies: [\"NucleicCore\"],\n26\t            resources: [.copy(\"Fixtures\")]\n27\t        ),\n28\t    ]\n29\t)\n30\t"

`#16` `raw[system/task_progress]` {"description":"Reading PLAN.md","last_tool_name":"Read","session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subagent_type":"Explore","subtype":"task_progress","task_id":"aa9eeac5fb94c0be0","tool_use_id":"toolu_01NeoJ35pHxaSHSepcpuJCLh","type":"system","usage":{"duration_ms":4510,"tool_uses":3,"total_tokens":10382},"uuid":"c5c5a029-d6be-46eb-b9cf-b07a68a3fa9c"}

`#18` **Tool** `Read` — {"file_path":"/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/PLAN.md","limit":100}

`#19` **Result**: "1\t# Nucleic — Plan\n2\t\n3\tA macOS app (codename **Nucleic**) that runs multiple Claude Code / Codex sessions in\n4\tparallel, each isolated in its own git worktree + branch, with a SwiftUI cockpit to start,\n5\twatch, approve, and merge them. A companion iPhone app connects to the Mac as a remote\n6\tclient to monitor sessions and answer approval prompts on the go.\n7\t\n8\tThe Mac is the **host** (does all real work: spawns CLIs, owns the repos). The iPhone is a\n9\t**thin remote client**. This host/client split is the spine of the whole design.\n10\t\n11\t## Locked decisions\n12\t\n13\t| Decision | Choice |\n14\t| --- | --- |\n15\t| Agents wrapped | Both Claude Code + Codex, behind one pluggable backend protocol |\n16\t| Concurrency model | Parallel git worktrees (the defining feature) |\n17\t| Agent integration | Wrap the CLI as a subprocess; parse `stream-json` output |\n18\t| Platforms | macOS (host) + iPhone (remote client) |\n19\t| iPhone role | Remote client to the Mac (monitor + approve) |\n20\t| Mac ↔ iPhone transport | LAN first; cloud relay fallback added later |\n21\t| Approvals | Interactive, per-session |\n22\t| Session resume | **Native CLI resume + a local transcript as the UI source of truth** |\n23\t| Distribution | **Deferred** — decide signing/notarization/MAS later |\n24\t| Relay hosting | **Build on Cloudflare, but later** — LAN-only for the first usable version |\n25\t\n26\t## Document set\n27\t\n28\tThis file is the hub and overview. Each layer is over-specified in its own doc:\n29\t\n30\t| Doc | Layer | Locks down |\n31\t| --- | --- | --- |\n32\t| [docs/BACKEND_PROTOCOL.md](docs/BACKEND_PROTOCOL.md) | Agent abstraction | `AgentBackend`, the normalized `AgentEvent` model, capability matrix, approval round-trip, per-CLI adapter mappings |\n33\t| [docs/ADAPTERS.md](docs/ADAPTERS.md) | Adapter internals | Claude in-process MCP approval server, Codex app-server JSON-RPC client, argv/JSON/method names, source-confirmed wire contracts |\n34\t|

`#20` `raw[system/task_progress]` {"description":"Running find /Users/blakeslee/Library/Mobile\\ Documents/c…","last_tool_name":"Bash","session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subagent_type":"Explore","subtype":"task_progress","task_id":"aa9eeac5fb94c0be0","tool_use_id":"toolu_01NeoJ35pHxaSHSepcpuJCLh","type":"system","usage":{"duration_ms":6027,"tool_uses":4,"total_tokens":13050},"uuid":"c656ab82-b838-4c35-959e-e22410401eff"}

`#22` **Tool** `Bash` — {"command":"find /Users/blakeslee/Library/Mobile\\ Documents/com~apple~CloudDocs/projects/nucleic/Sources -type f -name \"*.swift\" | head -20"}

`#23` **Result**: "/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/nucleic-spike/Spike.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/fake-claude/FakeClaude.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/JSONValue.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Session.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/ConversationExport.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/RiskClassifier.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/RandomName.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Transcript.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Backend.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Claude/ClaudeDecisionMapping.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Claude/ClaudeStreamDecoder.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Claude/ClaudeCodeBackend.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Claude/MCPApprovalServer.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/SessionController.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/AgentEvent.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Intelligence.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~Cl

`#24` `raw[system/task_notification]` {"output_file":"","session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","status":"completed","subtype":"task_notification","summary":"Quick repo overview","task_id":"aa9eeac5fb94c0be0","tool_use_id":"toolu_01NeoJ35pHxaSHSepcpuJCLh","type":"system","usage":{"duration_ms":13922,"tool_uses":4,"total_tokens":13983},"uuid":"cda2d58a-2fc9-41fa-b06b-f937b7485f35"}

`#25` **Result**: [{"text":"Perfect. Here's my concise overview:\n\n## Nucleic Repository Overview\n\n**What it is:** A macOS orchestration platform that runs multiple Claude Code and Codex agent sessions in parallel, each isolated in its own git worktree, with a SwiftUI \"cockpit\" for managing, approving, and merging agent-driven changes. A companion iPhone app serves as a remote client for monitoring and approving actions on-the-go.\n\n**Tech Stack:**\n- **Language:** Swift 6 with SwiftUI\n- **Platform:** macOS 14+ (host), iPhone (client)\n- **Database:** GRDB (SQLite wrapper)\n- **Transport:** Network.framework (Bonjour/LAN); Cloudflare relay planned for later\n\n**Main Components:**\n\n| Directory | Purpose |\n|---|---|\n| `Sources/NucleicCore/` | Core domain model, backend abstraction, agent event pipeline, session control |\n| `Sources/NucleicCore/Claude/` | Claude Code integration (CLI wrapper, stream JSON decoder, MCP approval server) |\n| `Sources/NucleicApp/` | macOS SwiftUI app (dashboard, session detail, approval UI) |\n| `Sources/nucleic-spike/` | Experimentation target |\n| `Sources/fake-claude/` | Test fixture to simulate agent behavior |\n| `Tests/` | Hermetic test suite with fixtures |\n| `docs/` | Comprehensive architecture specs (backend protocol, sync protocol, worktree management, runtime architecture, UX flows) |\n\n**Core Architecture:** Single-writer event pipeline with normalized `AgentEvent` stream. Local transcript is the source of truth. Pluggable `AgentBackend` protocol abstracts Claude Code and Codex. Mac host spawns subprocesses and owns git operations; iPhone client monitors via LAN sync.","type":"text"}]

`#26` **Assistant:** **Nucleic** is a macOS cockpit for running multiple AI coding agents (Claude Code, Codex) in parallel, each in its own git worktree. You manage, approve, and merge their changes from a SwiftUI dashboard; an iPhone companion app lets you monitor and approve remotely.

Key parts:
- **`NucleicCore/`** — domain model, session/worktree management, agent event pipeline, GRDB/SQLite persistence
- **`NucleicApp/`** — macOS SwiftUI dashboard (home, session detail, approval UI)
- **`Claude/`** — CLI subprocess wrapper + MCP approval server for Claude Code
- **`fake-claude/`** — test fixture simulating agent behavior
- **`docs/`** — detailed architecture specs for the backend protocol, sync, worktree management, etc.

Stack: Swift 6, SwiftUI, GRDB, Network.framework (Bonjour for LAN sync). Based on memory, M0 (foundation) is done and M1 (SessionController + WorktreeManager) backend core is complete with 75 tests — SwiftUI app work remains.

`#27` `raw[system/post_turn_summary]` {"needs_action":"","session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","status_category":"review_ready","status_detail":"Nucleic architecture overview: macOS+iOS agent cockpit with git worktree mgmt, SwiftUI dashboard, GRDB persistence, M0 done and M1 backend complete","subtype":"post_turn_summary","summarizes_uuid":"e80685d4-8956-4773-9d3d-dea0e9e28255","type":"system","uuid":"d1fdd1b1-5d85-44ec-ac66-2f91bf7246a6"}

`#28` _usage in=4 out=421_

`#29` _— turn completed —_

`#30` _— run completed —_

`#31` **User:** what has been completed thus far?

`#32` **session started** — model claude-sonnet-4-6

`#33` `raw[system/thinking_tokens]` {"estimated_tokens":1,"estimated_tokens_delta":1,"session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subtype":"thinking_tokens","type":"system","uuid":"1e505b56-54f8-46f6-9a87-10fb6d110823"}

`#34` `raw[system/thinking_tokens]` {"estimated_tokens":18,"estimated_tokens_delta":17,"session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subtype":"thinking_tokens","type":"system","uuid":"96a6a921-b25c-436e-b3f2-d7a5a64ad8d0"}

`#35` `raw[system/thinking_tokens]` {"estimated_tokens":20,"estimated_tokens_delta":2,"session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subtype":"thinking_tokens","type":"system","uuid":"d50fbc54-094d-4eb7-bbc3-6c8bd2f47062"}

`#36` `raw[system/thinking_tokens]` {"estimated_tokens":71,"estimated_tokens_delta":51,"session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subtype":"thinking_tokens","type":"system","uuid":"4e0a1c77-e5e7-4ce7-ad75-d76d603d3d5f"}

`#39` **Tool** `Read` — {"file_path":"/Users/blakeslee/.claude/projects/-Users-blakeslee-Library-Mobile-Documents-com-apple-CloudDocs-projects-nucleic/memory/nucleic-m0-state.md"}

`#40` **Result**: "1\t---\n2\tname: nucleic-m0-state\n3\tdescription: Nucleic M0 spike completed 2026-06-12; key adapter finding about --permission-mode\n4\tmetadata: \n5\t  node_type: memory\n6\t  type: project\n7\t  originSessionId: 0eb2ba83-e10f-45c5-8d06-534091433155\n8\t---\n9\t\n10\tM0 (PLAN.md milestone 1) was completed 2026-06-12 on branch `claude/optimistic-lalande-a30279`:\n11\tNucleicCore package + nucleic-spike CLI + fake-claude stub, 41 hermetic tests, live captures\n12\tcommitted under `fixtures/claude/2.1.167/`. Full findings in `docs/M0_RESULTS.md`.\n13\t\n14\t**Why this matters for M1:** the live capture exposed that a user-level\n15\t`defaultMode: \"auto\"` in `~/.claude/settings.json` auto-accepts edits BEFORE the\n16\t`--permission-prompt-tool` is consulted — the adapter must pin `--permission-mode default`\n17\tfor interactive sessions (already implemented in ClaudeCodeBackend). Also: the spawned CLI\n18\tinherits the host's global plugins/MCP servers; M1 should consider `--strict-mcp-config`.\n19\t\n20\t**How to apply:** M1 starts with SessionController + WorktreeManager (see M0_RESULTS \"What\n21\tM1 should pick up first\"). Build with [[icloud-swiftbuild-codesign]] workaround.\n22\t"

`#42` **Tool** `Read` — {"file_path":"/Users/blakeslee/.claude/projects/-Users-blakeslee-Library-Mobile-Documents-com-apple-CloudDocs-projects-nucleic/memory/nucleic-m1-state.md"}

`#43` **Result**: "1\t---\n2\tname: nucleic-m1-state\n3\tdescription: \"Nucleic M1 core spine completed 2026-06-12; what's built, key decisions, what remains (SwiftUI app)\"\n4\tmetadata: \n5\t  node_type: memory\n6\t  type: project\n7\t  originSessionId: b76e66d6-1d01-400e-a729-5a55550aa619\n8\t---\n9\t\n10\tM1 (PLAN \"Single-session macOS MVP\") — **backend core spine complete** 2026-06-12 on\n11\tbranch `claude/laughing-buck-c3b99c`. 75 tests green via `swift test --build-system native`\n12\t([[icloud-swiftbuild-codesign]]). Follows [[nucleic-m0-state]].\n13\t\n14\t**First commit landed M0**: the M0 deliverable was never actually committed — it sat\n15\tuncommitted in the sibling `optimistic-lalande` worktree. First M1 commit brought it onto\n16\tthis branch as the baseline (memory said \"committed\" but it wasn't).\n17\t\n18\t**Built (all in `Sources/NucleicCore/`):**\n19\t- `Git/GitRunner.swift` + `Git/WorktreeManager.swift` — `GitWorktreeManager` actor:\n20\t  create/status/diff/finalize/integrate/discard/reconcile. `Project`/`GitRef`/`Slug` in\n21\t  `Project.swift`.\n22\t- `Session.swift` + `SessionController.swift` — single-writer pipeline (RUNTIME §2):\n23\t  consumes backend stream, canonical seq via TranscriptWriter, status state machine, fan-out,\n24\t  approval bridge, integrate intents. `join()` awaits run completion.\n25\t- `AgentEvent.Kind.rateLimit` models `rate_limit_event` (M0 finding 6).\n26\t  `ClaudeCodeBackend.Configuration.strictMCPConfig` (default on) → `--strict-mcp-config`\n27\t  (M0 finding 7).\n28\t- `Persistence/` — `SessionMetadataStore` protocol + `GRDBMetadataStore` (**GRDB 7.11, the\n29\t  first external dep**; resolves+builds fine under native build system).\n30\t\n31\t**Key decisions (don't re-litigate):**\n32\t- `GitRunner` awaits process exit via the **termination handler, NOT `waitUntilExit()`** —\n33\t  the latter blocks a Swift-concurrency cooperative thread and deadlocks under parallel\n34\t  callers (swift-testing runs @Tests in parallel). 

`#44` _rate limit five_hour allowed_

`#45` **Assistant:** Here's a summary of what's been built:

## M0 — Foundation (done 2026-06-12)
- `NucleicCore` Swift package + `nucleic-spike` CLI + `fake-claude` stub
- 41 hermetic tests, live capture fixtures
- Key finding: must pin `--permission-mode default` to prevent auto-accept before the permission prompt tool fires

## M1 — Single-Session macOS MVP (backend + app both done 2026-06-12, 80 tests)

**Backend core:**
- `WorktreeManager` — create/status/diff/finalize/integrate/discard/reconcile
- `SessionController` — single-writer event pipeline, status state machine, approval bridge
- `GRDBMetadataStore` — SQLite persistence via GRDB
- Turn-by-turn chat via one single-shot process per turn (`claude --resume <id>`) — stdin-open + permission-prompt-tool hangs, so this is the working model

**SwiftUI app:**
- Home dashboard with greeting, stat cards, GitHub-style activity grid
- Session detail: transcript (chat bubbles), diffstat, approval bar
- Per-session model/effort pickers, Stop (interrupt) control
- Project management: dedup, rename, cascade delete; session rename, favorite, archive, delete
- AI features via Apple Foundation Models: auto session naming + conversation summary cards; Settings picker for On-Device / PCC / Off
- Session reload on launch (replays transcript, rebuilds idle controllers)
- Auto mode (`--permission-mode auto`) toggle per chat + global default

**Remaining M1 polish (not yet done):**
- Live diff *patch* pane (only diffstat shown today)
- Menu-bar item + notifications

`#46` `raw[system/post_turn_summary]` {"needs_action":"","session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","status_category":"review_ready","status_detail":"M0 & M1 complete (80 tests); backend core + SwiftUI app shipped; remaining: live diff patch pane + menu-bar/notifications","subtype":"post_turn_summary","summarizes_uuid":"05a87568-c129-4675-96f7-94be0bd73d8e","type":"system","uuid":"671bd778-1069-4b09-aea5-18a76960bbed"}

`#47` _usage in=4 out=626_

`#48` _— turn completed —_

`#49` _— run completed —_

`#50` **User:** what should we do next?

`#51` **session started** — model claude-sonnet-4-6

`#52` `raw[system/thinking_tokens]` {"estimated_tokens":1,"estimated_tokens_delta":1,"session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subtype":"thinking_tokens","type":"system","uuid":"99467102-4670-4e4f-aab7-21e180b3a124"}

`#53` `raw[system/thinking_tokens]` {"estimated_tokens":14,"estimated_tokens_delta":13,"session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subtype":"thinking_tokens","type":"system","uuid":"c71d4bba-a319-461e-bec7-60886674f2f4"}

`#54` `raw[system/thinking_tokens]` {"estimated_tokens":65,"estimated_tokens_delta":51,"session_id":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","subtype":"thinking_tokens","type":"system","uuid":"f3870790-4e91-4c19-9018-030013f72860"}

`#57` **Tool** `Glob` — {"path":"/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic","pattern":"docs/PLAN*.md"}

`#58` _rate limit five_hour allowed_

`#59` **Result**: "No files found"

`#61` **Tool** `Glob` — {"path":"/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic","pattern":"*.md"}

`#62` **Result**: "docs/BACKEND_PROTOCOL.md\ndocs/OBSERVABILITY_AND_TESTING.md\ndocs/RUNTIME_ARCHITECTURE.md\ndocs/SYNC_PROTOCOL.md\ndocs/UX_IOS.md\ndocs/UX_MACOS.md\ndocs/WORKTREE_MANAGER.md\n.claude/worktrees/optimistic-lalande-a30279/docs/BACKEND_PROTOCOL.md\n.claude/worktrees/optimistic-lalande-a30279/docs/OBSERVABILITY_AND_TESTING.md\n.claude/worktrees/optimistic-lalande-a30279/docs/RUNTIME_ARCHITECTURE.md\n.claude/worktrees/optimistic-lalande-a30279/docs/SYNC_PROTOCOL.md\n.claude/worktrees/optimistic-lalande-a30279/docs/UX_IOS.md\n.claude/worktrees/optimistic-lalande-a30279/docs/UX_MACOS.md\n.claude/worktrees/optimistic-lalande-a30279/docs/WORKTREE_MANAGER.md\n.claude/worktrees/laughing-buck-c3b99c/docs/M0_RESULTS.md\n.claude/worktrees/optimistic-lalande-a30279/docs/M0_RESULTS.md\n.claude/worktrees/laughing-buck-c3b99c/PLAN.md\n.claude/worktrees/optimistic-lalande-a30279/PLAN.md\n.claude/worktrees/laughing-buck-c3b99c/docs/ADAPTERS.md\n.claude/worktrees/optimistic-lalande-a30279/docs/ADAPTERS.md\n.claude/worktrees/laughing-buck-c3b99c/docs/BACKEND_PROTOCOL.md\n.claude/worktrees/laughing-buck-c3b99c/docs/OBSERVABILITY_AND_TESTING.md\n.claude/worktrees/laughing-buck-c3b99c/docs/RUNTIME_ARCHITECTURE.md\n.claude/worktrees/laughing-buck-c3b99c/docs/SYNC_PROTOCOL.md\n.claude/worktrees/laughing-buck-c3b99c/docs/UX_IOS.md\n.claude/worktrees/laughing-buck-c3b99c/docs/UX_MACOS.md\n.claude/worktrees/laughing-buck-c3b99c/docs/WORKTREE_MANAGER.md\n.claude/worktrees/laughing-buck-c3b99c/.build/checkouts/GRDB.swift/.github/ISSUE_TEMPLATE.md\n.claude/worktrees/laughing-buck-c3b99c/.build/checkouts/GRDB.swift/.github/PULL_REQUEST_TEMPLATE.md\n.claude/worktrees/laughing-buck-c3b99c/.build/checkouts/GRDB.swift/BRAG.md\n.claude/worktrees/laughing-buck-c3b99c/.build/checkouts/GRDB.swift/CHANGELOG.md\n.claude/worktrees/laughing-buck-c3b99c/.build/checkouts/GRDB.swift/CODE_OF_CONDUCT.md\n.claude/worktrees/laughing-buck-c3b99c/.build/checkouts/GRDB.swift/CONTRIBUTING.md\n.claude/worktrees/laughing-buc

`#64` **Tool** `Read` — {"file_path":"/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/.claude/worktrees/laughing-buck-c3b99c/PLAN.md"}

`#65` `raw[?]` "{\"type\":\"user\",\"message\":{\"role\":\"user\",\"content\":[{\"tool_use_id\":\"toolu_01BppistjQkUv7p7u6UuRtDM\",\"type\":\"tool_result\",\"content\":\"1\\t# Nucleic — Plan\\n2\\t\\n3\\tA macOS app (codename **Nucleic**) that runs multiple Claude Code / Codex sessions in\\n4\\tparallel, each isolated in its own git worktree + branch, with a SwiftUI cockpit to start,\\n5\\twatch, approve, and merge them. A companion iPhone app connects to the Mac as a remote\\n6\\tclient to monitor sessions an

`#66` _— run completed —_


## Raw events (JSONL)

Full normalized event stream for debugging:

```jsonl
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{"at":"2026-06-12T23:13:44Z","backend":"claudeCode","kind":{"content":"1\t// swift-tools-version: 6.0\n2\timport PackageDescription\n3\t\n4\tlet package = Package(\n5\t    name: \"Nucleic\",\n6\t    platforms: [.macOS(.v14)],\n7\t    products: [\n8\t        .library(name: \"NucleicCore\", targets: [\"NucleicCore\"]),\n9\t        .executable(name: \"NucleicApp\", targets: [\"NucleicApp\"]),\n10\t        .executable(name: \"nucleic-spike\", targets: [\"nucleic-spike\"]),\n11\t        .executable(name: \"fake-claude\", targets: [\"fake-claude\"]),\n12\t    ],\n13\t    dependencies: [\n14\t        .package(url: \"https://github.com/groue/GRDB.swift.git\", from: \"7.0.0\"),\n15\t    ],\n16\t    targets: [\n17\t        .target(\n18\t            name: \"NucleicCore\",\n19\t            dependencies: [.product(name: \"GRDB\", package: \"GRDB.swift\")]),\n20\t        .executableTarget(name: \"NucleicApp\", dependencies: [\"NucleicCore\"]),\n21\t        .executableTarget(name: \"nucleic-spike\", dependencies: [\"NucleicCore\"]),\n22\t        .executableTarget(name: \"fake-claude\", dependencies: [\"NucleicCore\"]),\n23\t        .testTarget(\n24\t            name: \"NucleicCoreTests\",\n25\t            dependencies: [\"NucleicCore\"],\n26\t            resources: [.copy(\"Fixtures\")]\n27\t        ),\n28\t    ]\n29\t)\n30\t","isError":false,"toolCallID":"toolu_012pn2S5fiZAjQwkHXvuVbMW","type":"toolResult"},"nativeType":"user","seq":15,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
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{"at":"2026-06-12T23:13:44Z","backend":"claudeCode","kind":{"content":"1\t# Nucleic — Plan\n2\t\n3\tA macOS app (codename **Nucleic**) that runs multiple Claude Code / Codex sessions in\n4\tparallel, each isolated in its own git worktree + branch, with a SwiftUI cockpit to start,\n5\twatch, approve, and merge them. A companion iPhone app connects to the Mac as a remote\n6\tclient to monitor sessions and answer approval prompts on the go.\n7\t\n8\tThe Mac is the **host** (does all real work: spawns CLIs, owns the repos). The iPhone is a\n9\t**thin remote client**. This host/client split is the spine of the whole design.\n10\t\n11\t## Locked decisions\n12\t\n13\t| Decision | Choice |\n14\t| --- | --- |\n15\t| Agents wrapped | Both Claude Code + Codex, behind one pluggable backend protocol |\n16\t| Concurrency model | Parallel git worktrees (the defining feature) |\n17\t| Agent integration | Wrap the CLI as a subprocess; parse `stream-json` output |\n18\t| Platforms | macOS (host) + iPhone (remote client) |\n19\t| iPhone role | Remote client to the Mac (monitor + approve) |\n20\t| Mac ↔ iPhone transport | LAN first; cloud relay fallback added later |\n21\t| Approvals | Interactive, per-session |\n22\t| Session resume | **Native CLI resume + a local transcript as the UI source of truth** |\n23\t| Distribution | **Deferred** — decide signing/notarization/MAS later |\n24\t| Relay hosting | **Build on Cloudflare, but later** — LAN-only for the first usable version |\n25\t\n26\t## Document set\n27\t\n28\tThis file is the hub and overview. Each layer is over-specified in its own doc:\n29\t\n30\t| Doc | Layer | Locks down |\n31\t| --- | --- | --- |\n32\t| [docs/BACKEND_PROTOCOL.md](docs/BACKEND_PROTOCOL.md) | Agent abstraction | `AgentBackend`, the normalized `AgentEvent` model, capability matrix, approval round-trip, per-CLI adapter mappings |\n33\t| [docs/ADAPTERS.md](docs/ADAPTERS.md) | Adapter internals | Claude in-process MCP approval server, Codex app-server JSON-RPC client, argv/JSON/method names, source-confirmed wire contracts |\n34\t| [docs/SYNC_PROTOCOL.md](docs/SYNC_PROTOCOL.md) | Mac ↔ iPhone | `ClientMsg`/`HostMsg`, `seq`-cursor catch-up, E2EE pairing (`SecureChannel`), first-responder approvals, verbosity throttling |\n35\t| [docs/WORKTREE_MANAGER.md](docs/WORKTREE_MANAGER.md) | Git | Worktree lifecycle, diff plumbing, merge/rebase/squash/PR + conflicts, crash reconciliation |\n36\t| [docs/RUNTIME_ARCHITECTURE.md](docs/RUNTIME_ARCHITECTURE.md) | Integration | Object graph, single-writer event pipeline, GRDB schema, approval bridging, Swift 6 concurrency |\n37\t| [docs/UX_MACOS.md](docs/UX_MACOS.md) | macOS UX | Navigation, dashboard, session detail, approval bar, create/approve/integrate flows |\n38\t| [docs/UX_IOS.md](docs/UX_IOS.md) | iPhone UX | Notification-first IA, approval flows, connectivity states, biometric gating |\n39\t| [docs/OBSERVABILITY_AND_TESTING.md](docs/OBSERVABILITY_AND_TESTING.md) | Cross-cutting | Local-first redaction-aware observability + hermetic test pyramid with fake-CLI fixtures |\n40\t\n41\t**The spine across all of them:** one normalized `AgentEvent` stream with a canonical monotonic\n42\t`seq`, written once by the `SessionController` (single writer), with the local transcript as the\n43\tsource of truth — UI, sync, and persistence are all subscribers. Every backend/transport\n44\tdifference is a declared *capability*, never an assumption. The single seam that unifies two very\n45\tdifferent approval mechanisms is `ApprovalCoordinator.await(...) -> Decision`.\n46\t\n47\t## Architecture\n48\t\n49\t```\n50\t┌───────────────────────── macOS host ─────────────────────────┐\n51\t│  SwiftUI app                                                  │\n52\t│  ┌──────────────┐   ┌────────────────────┐  ┌──────────────┐  │\n53\t│  │ Session UI   │   │ AgentBackend layer │  │ Git/Worktree │  │\n54\t│  │ (panes,diff, │◄─►│  ClaudeCodeBackend │  │   manager    │  │\n55\t│  │  approvals)  │   │  CodexBackend      │  └──────┬───────┘  │\n56\t│  └──────┬───────┘   └─────────┬──────────┘         │          │\n57\t│         │                     │ spawns + stream-json│         │\n58\t│         │            ┌────────▼────────┐    ┌───────▼───────┐ │\n59\t│         │            │ child processes │    │  git worktrees│ │\n60\t│         │            │ claude / codex  │    │  + branches   │ │\n61\t│         │            └─────────────────┘    └───────────────┘ │\n62\t│         │                                                     │\n63\t│  ┌──────▼──────────────── Sync server ──────────────────────┐ │\n64\t│  │  Network.framework (Bonjour/LAN)  +  relay client (later)│ │\n65\t│  └──────────────────────────┬──────────────────────────────┘ │\n66\t└─────────────────────────────┼────────────────────────────────┘\n67\t                              LAN  ╲  relay fallback (Cloudflare, later)\n68\t                               │    ╲\n69\t                        ┌──────▼─────────────┐\n70\t                        │   iPhone client     │\n71\t                        │ monitor + approve   │\n72\t                        └─────────────────────┘\n73\t```\n74\t\n75\t## Core domain model\n76\t\n77\tA small, backend-agnostic model everything else is built on.\n78\t\n79\t- **Project** — a registered git repo (root path, default branch, per-project config:\n80\t  setup script, approval defaults, default backend).\n81\t- **Session** — one agent run. Belongs to a Project, owns a **Worktree**, has a backend\n82\t  type, status (`idle / running / awaiting-approval / awaiting-input / finished / error`),\n83\t  and a transcript.\n84\t- **Worktree** — `path`, `branch`, base commit, dirty/clean, ahead/behind counts.\n85\t- **TranscriptEvent** — the normalized event stream (see backend section). Stored as JSONL\n86\t  on disk; metadata in the DB. **This local transcript is the UI's source of truth.**\n87\t- **ApprovalRequest** — tool name, input, risk, owning session; resolved with allow/deny\n88\t  (+ optional \"always for this tool/session\").\n89\t\n90\t## Pluggable agent backend (highest-leverage abstraction)\n91\t\n92\tOne protocol normalizes two genuinely different CLIs:\n93\t\n94\t```swift\n95\tprotocol AgentBackend {\n96\t    func start(in worktree: Worktree, prompt: String, opts: RunOptions) -> AsyncStream<AgentEvent>\n97\t    func send(_ input: AgentInput)          // follow-up turns\n98\t    func respond(to: ApprovalRequest, _ decision: Decision)\n99\t    func interrupt()\n100\t    func resume(sessionID: String) -> AsyncStream<AgentEvent>","isError":false,"toolCallID":"toolu_01LBN5XFHbvCysJMCuLqGTPw","type":"toolResult"},"nativeType":"user","seq":19,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
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{"at":"2026-06-12T23:13:44Z","backend":"claudeCode","kind":{"content":"/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/nucleic-spike/Spike.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/fake-claude/FakeClaude.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/JSONValue.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Session.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/ConversationExport.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/RiskClassifier.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/RandomName.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Transcript.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Backend.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Claude/ClaudeDecisionMapping.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Claude/ClaudeStreamDecoder.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Claude/ClaudeCodeBackend.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Claude/MCPApprovalServer.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/SessionController.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/AgentEvent.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Intelligence.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/ProcessHost.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Project.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Persistence/SessionMetadataStore.swift\n/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/Sources/NucleicCore/Persistence/GRDBMetadataStore.swift","isError":false,"toolCallID":"toolu_01HwujWxfFkguaA7BV3DbdpM","type":"toolResult"},"nativeType":"user","seq":23,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
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{"at":"2026-06-12T23:13:44Z","backend":"claudeCode","kind":{"content":[{"text":"Perfect. Here's my concise overview:\n\n## Nucleic Repository Overview\n\n**What it is:** A macOS orchestration platform that runs multiple Claude Code and Codex agent sessions in parallel, each isolated in its own git worktree, with a SwiftUI \"cockpit\" for managing, approving, and merging agent-driven changes. A companion iPhone app serves as a remote client for monitoring and approving actions on-the-go.\n\n**Tech Stack:**\n- **Language:** Swift 6 with SwiftUI\n- **Platform:** macOS 14+ (host), iPhone (client)\n- **Database:** GRDB (SQLite wrapper)\n- **Transport:** Network.framework (Bonjour/LAN); Cloudflare relay planned for later\n\n**Main Components:**\n\n| Directory | Purpose |\n|---|---|\n| `Sources/NucleicCore/` | Core domain model, backend abstraction, agent event pipeline, session control |\n| `Sources/NucleicCore/Claude/` | Claude Code integration (CLI wrapper, stream JSON decoder, MCP approval server) |\n| `Sources/NucleicApp/` | macOS SwiftUI app (dashboard, session detail, approval UI) |\n| `Sources/nucleic-spike/` | Experimentation target |\n| `Sources/fake-claude/` | Test fixture to simulate agent behavior |\n| `Tests/` | Hermetic test suite with fixtures |\n| `docs/` | Comprehensive architecture specs (backend protocol, sync protocol, worktree management, runtime architecture, UX flows) |\n\n**Core Architecture:** Single-writer event pipeline with normalized `AgentEvent` stream. Local transcript is the source of truth. Pluggable `AgentBackend` protocol abstracts Claude Code and Codex. Mac host spawns subprocesses and owns git operations; iPhone client monitors via LAN sync.","type":"text"}],"isError":false,"toolCallID":"toolu_01NeoJ35pHxaSHSepcpuJCLh","type":"toolResult"},"nativeType":"user","seq":25,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
{"at":"2026-06-12T23:13:44Z","backend":"claudeCode","kind":{"isPartial":false,"messageID":"msg_01WmpEyJNmCFKsT4sUQfVEJn","text":"**Nucleic** is a macOS cockpit for running multiple AI coding agents (Claude Code, Codex) in parallel, each in its own git worktree. You manage, approve, and merge their changes from a SwiftUI dashboard; an iPhone companion app lets you monitor and approve remotely.\n\nKey parts:\n- **`NucleicCore/`** — domain model, session/worktree management, agent event pipeline, GRDB/SQLite persistence\n- **`NucleicApp/`** — macOS SwiftUI dashboard (home, session detail, approval UI)\n- **`Claude/`** — CLI subprocess wrapper + MCP approval server for Claude Code\n- **`fake-claude/`** — test fixture simulating agent behavior\n- **`docs/`** — detailed architecture specs for the backend protocol, sync, worktree management, etc.\n\nStack: Swift 6, SwiftUI, GRDB, Network.framework (Bonjour for LAN sync). Based on memory, M0 (foundation) is done and M1 (SessionController + WorktreeManager) backend core is complete with 75 tests — SwiftUI app work remains.","type":"assistantText"},"nativeType":"assistant","seq":26,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
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{"at":"2026-06-12T23:15:55Z","backend":"claudeCode","kind":{"isPartial":false,"messageID":"user-2","text":"what has been completed thus far?","type":"userText"},"seq":31,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
{"at":"2026-06-12T23:15:56Z","backend":"claudeCode","kind":{"backendSessionID":"c29d82c3-3baa-4f88-b8d1-04151486ebe4","cwd":"/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic","model":"claude-sonnet-4-6","toolNames":["Task","AskUserQuestion","Bash","CronCreate","CronDelete","CronList","DesignSync","Edit","EnterPlanMode","EnterWorktree","ExitPlanMode","ExitWorktree","Glob","Grep","LSP","Monitor","NotebookEdit","PushNotification","Read","RemoteTrigger","ScheduleWakeup","Skill","TaskCreate","TaskGet","TaskList","TaskOutput","TaskStop","TaskUpdate","ToolSearch","WebFetch","WebSearch","Workflow","Write"],"type":"sessionStarted"},"nativeType":"system/init","seq":32,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
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{"at":"2026-06-12T23:16:12Z","backend":"claudeCode","kind":{"isPartial":false,"messageID":"msg_01YRUYNmcPKAdz7JKpBmoW4B","text":"Let me check the memory files and also look at docs/specs for current state.","type":"thinking"},"nativeType":"assistant","seq":37,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
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{"at":"2026-06-12T23:16:12Z","backend":"claudeCode","kind":{"content":"1\t---\n2\tname: nucleic-m0-state\n3\tdescription: Nucleic M0 spike completed 2026-06-12; key adapter finding about --permission-mode\n4\tmetadata: \n5\t  node_type: memory\n6\t  type: project\n7\t  originSessionId: 0eb2ba83-e10f-45c5-8d06-534091433155\n8\t---\n9\t\n10\tM0 (PLAN.md milestone 1) was completed 2026-06-12 on branch `claude/optimistic-lalande-a30279`:\n11\tNucleicCore package + nucleic-spike CLI + fake-claude stub, 41 hermetic tests, live captures\n12\tcommitted under `fixtures/claude/2.1.167/`. Full findings in `docs/M0_RESULTS.md`.\n13\t\n14\t**Why this matters for M1:** the live capture exposed that a user-level\n15\t`defaultMode: \"auto\"` in `~/.claude/settings.json` auto-accepts edits BEFORE the\n16\t`--permission-prompt-tool` is consulted — the adapter must pin `--permission-mode default`\n17\tfor interactive sessions (already implemented in ClaudeCodeBackend). Also: the spawned CLI\n18\tinherits the host's global plugins/MCP servers; M1 should consider `--strict-mcp-config`.\n19\t\n20\t**How to apply:** M1 starts with SessionController + WorktreeManager (see M0_RESULTS \"What\n21\tM1 should pick up first\"). Build with [[icloud-swiftbuild-codesign]] workaround.\n22\t","isError":false,"toolCallID":"toolu_01GKqMnAKrQhSbJZoq6tEuud","type":"toolResult"},"nativeType":"user","seq":40,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
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{"at":"2026-06-12T23:16:12Z","backend":"claudeCode","kind":{"content":"1\t---\n2\tname: nucleic-m1-state\n3\tdescription: \"Nucleic M1 core spine completed 2026-06-12; what's built, key decisions, what remains (SwiftUI app)\"\n4\tmetadata: \n5\t  node_type: memory\n6\t  type: project\n7\t  originSessionId: b76e66d6-1d01-400e-a729-5a55550aa619\n8\t---\n9\t\n10\tM1 (PLAN \"Single-session macOS MVP\") — **backend core spine complete** 2026-06-12 on\n11\tbranch `claude/laughing-buck-c3b99c`. 75 tests green via `swift test --build-system native`\n12\t([[icloud-swiftbuild-codesign]]). Follows [[nucleic-m0-state]].\n13\t\n14\t**First commit landed M0**: the M0 deliverable was never actually committed — it sat\n15\tuncommitted in the sibling `optimistic-lalande` worktree. First M1 commit brought it onto\n16\tthis branch as the baseline (memory said \"committed\" but it wasn't).\n17\t\n18\t**Built (all in `Sources/NucleicCore/`):**\n19\t- `Git/GitRunner.swift` + `Git/WorktreeManager.swift` — `GitWorktreeManager` actor:\n20\t  create/status/diff/finalize/integrate/discard/reconcile. `Project`/`GitRef`/`Slug` in\n21\t  `Project.swift`.\n22\t- `Session.swift` + `SessionController.swift` — single-writer pipeline (RUNTIME §2):\n23\t  consumes backend stream, canonical seq via TranscriptWriter, status state machine, fan-out,\n24\t  approval bridge, integrate intents. `join()` awaits run completion.\n25\t- `AgentEvent.Kind.rateLimit` models `rate_limit_event` (M0 finding 6).\n26\t  `ClaudeCodeBackend.Configuration.strictMCPConfig` (default on) → `--strict-mcp-config`\n27\t  (M0 finding 7).\n28\t- `Persistence/` — `SessionMetadataStore` protocol + `GRDBMetadataStore` (**GRDB 7.11, the\n29\t  first external dep**; resolves+builds fine under native build system).\n30\t\n31\t**Key decisions (don't re-litigate):**\n32\t- `GitRunner` awaits process exit via the **termination handler, NOT `waitUntilExit()`** —\n33\t  the latter blocks a Swift-concurrency cooperative thread and deadlocks under parallel\n34\t  callers (swift-testing runs @Tests in parallel). Apply this pattern to any new subprocess code.\n35\t- `integrate()` lands in the **main checkout** (guarded clean, §6.2), NOT a detached-worktree\n36\t  + `update-ref` bump — a ref bump on a checked-out branch desyncs the working copy.\n37\t- Tests build temp git repos under `NSTemporaryDirectory()` (outside iCloud) to dodge the\n38\t  provenance-xattr codesign issue.\n39\t\n40\t**App target built** (2026-06-12): `AppStore` (@MainActor @Observable, in NucleicCore, RUNTIME §1)\n41\tties Project + Database + WorktreeManager + SessionController; `createSession` does\n42\tworktree+transcript+controller+persist+start; observes each controller's stream. Plus a\n43\t`NucleicApp` SwiftUI executable target (sidebar, session detail w/ transcript + diffstat +\n44\tapproval bar, new-session/add-project sheets). Run: `swift run --build-system native NucleicApp`\n45\t(store under `~/Library/Application Support/Nucleic`). 78 tests green.\n46\t\n47\t**Turn-by-turn chat done** (2026-06-12). `AgentEvent.Kind.userText` carries the user's message\n48\t(the CLI doesn't echo input) — SessionController injects it on start + each turn. UI has a chat\n49\tcomposer (user msgs = trailing bubbles), a per-project \"+\" that opens a randomly-named chat\n50\t([[RandomName]], three words e.g. `amber-quiet-otter`) straight into the chat view, and an agent\n51\t**Stop** (interrupt) control. New chats create the worktree up front; the agent runs on the first\n52\tmessage.\n53\t\n54\t⚠️ **CRITICAL BACKEND FINDING (don't re-break):** Claude's **streaming-input mode (stdin kept\n55\topen) HANGS when combined with `--permission-prompt-tool`** — it emits `init` then produces\n56\tnothing, forever. Reproduced 3 ways: single-shot + approval server ✅; open-stdin, no approval\n57\tserver ✅; **open-stdin + approval server ✖ (hang)**. So chat must NOT keep stdin open. The\n58\tworking model is **one single-shot process PER TURN** (`closeStdinAfterPrompt: true`), first via\n59\t`start`, follow-ups via `claude --resume <id>` carrying the message (verified retains context:\n60\t\"ZORP\" test). `ResumeSpec.prompt` carries the follow-up; `SessionController(conversational: true)`\n61\tmakes a turn's terminal `runFinished` mean *awaitingInput* (session stays alive), `sendInput`\n62\tresumes. `result(success)` still decodes to `turnCompleted`. Debug: set `NUCLEIC_DEBUG_STDERR=1`\n63\tto surface child stderr; spike has `--keep-stdin` to repro the hang. 80 tests green.\n64\t\n65\t**App now has:** home dashboard (greeting + stat cards + GitHub-style activity grid from\n66\tper-day user-message counts), per-session model/effort pickers (real `--model`/`--effort`),\n67\tproject dedup + rename + cascade delete, session rename. AI features via Apple Foundation Models\n68\t(`IntelligenceProviding` seam in core, `AppleIntelligenceProvider` in app): model-generated\n69\tconversation summary card + auto session names from the first message; Settings (⌘,) picks\n70\tOn-Device / Private Cloud Compute / Off.\n71\t\n72\t⚠️ **FoundationModels gotcha:** `SystemLanguageModel` is **macOS 26+**, but\n73\t`PrivateCloudComputeLanguageModel` and the generic `LanguageModelSession(model: some LanguageModel)`\n74\tinit are **macOS 27+** — gate them separately (`#available(macOS 27)`), and wrap the whole thing in\n75\t`#if canImport(FoundationModels)`. Both models conform to `LanguageModel`; drive either via\n76\t`LanguageModelSession(model:instructions:).respond(to:).content`. Any unavailability/error falls\n77\tback to `HeuristicIntelligence`. SDK = Xcode-beta (macOS 27 SDK).\n78\t\n79\t**Session reload on launch:** `AppStore.loadSessions()` (called after `loadProjects` in the app's\n80\t`.task`) rebuilds an idle resumable `SessionController` per DB session, replaying its transcript\n81\t(`TranscriptWriter.init(appendingTo:lastSeq:)` + `SessionController(initialHistory:)`). Without it\n82\tchats vanished from the sidebar after relaunch while the dashboard still counted them.\n83\t\n84\t**Auto mode = Claude's built-in `--permission-mode auto`** (NOT our own classifier). `claude` has\n85\tmodes `default/acceptEdits/auto/bypassPermissions/dontAsk/plan` + an `auto-mode` subcommand\n86\t(\"Inspect auto mode classifier\"). In `auto`, Claude auto-approves safe actions and routes\n87\tdestructive ones to our `--permission-prompt-tool`, giving \"all but destructive\" with everything\n88\tstill in the transcript. `Session.auto` → `RunSpec/ResumeSpec.autoApprove` → backend swaps\n89\t`--permission-mode default`↔`auto`. 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{"at":"2026-06-12T23:34:40Z","backend":"claudeCode","kind":{"isPartial":false,"messageID":"msg_01PK1aDDDzdAeMmV7ThRPDE8","text":"Let me check the PLAN.md to see what's planned next.","type":"thinking"},"nativeType":"assistant","seq":55,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
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{"at":"2026-06-12T23:34:40Z","backend":"claudeCode","kind":{"native":"{\"type\":\"user\",\"message\":{\"role\":\"user\",\"content\":[{\"tool_use_id\":\"toolu_01BppistjQkUv7p7u6UuRtDM\",\"type\":\"tool_result\",\"content\":\"1\\t# Nucleic — Plan\\n2\\t\\n3\\tA macOS app (codename **Nucleic**) that runs multiple Claude Code / Codex sessions in\\n4\\tparallel, each isolated in its own git worktree + branch, with a SwiftUI cockpit to start,\\n5\\twatch, approve, and merge them. A companion iPhone app connects to the Mac as a remote\\n6\\tclient to monitor sessions and answer approval prompts on the go.\\n7\\t\\n8\\tThe Mac is the **host** (does all real work: spawns CLIs, owns the repos). The iPhone is a\\n9\\t**thin remote client**. This host/client split is the spine of the whole design.\\n10\\t\\n11\\t## Locked decisions\\n12\\t\\n13\\t| Decision | Choice |\\n14\\t| --- | --- |\\n15\\t| Agents wrapped | Both Claude Code + Codex, behind one pluggable backend protocol |\\n16\\t| Concurrency model | Parallel git worktrees (the defining feature) |\\n17\\t| Agent integration | Wrap the CLI as a subprocess; parse `stream-json` output |\\n18\\t| Platforms | macOS (host) + iPhone (remote client) |\\n19\\t| iPhone role | Remote client to the Mac (monitor + approve) |\\n20\\t| Mac ↔ iPhone transport | LAN first; cloud relay fallback added later |\\n21\\t| Approvals | Interactive, per-session |\\n22\\t| Session resume | **Native CLI resume + a local transcript as the UI source of truth** |\\n23\\t| Distribution | **Deferred** — decide signing/notarization/MAS later |\\n24\\t| Relay hosting | **Build on Cloudflare, but later** — LAN-only for the first usable version |\\n25\\t\\n26\\t## Document set\\n27\\t\\n28\\tThis file is the hub and overview. Each layer is over-specified in its own doc:\\n29\\t\\n30\\t| Doc | Layer | Locks down |\\n31\\t| --- | --- | --- |\\n32\\t| [docs/BACKEND_PROTOCOL.md](docs/BACKEND_PROTOCOL.md) | Agent abstraction | `AgentBackend`, the normalized `AgentEvent` model, capability matrix, approval round-trip, per-CLI adapter mappings |\\n33\\t| [docs/ADAPTERS.md](docs/ADAPTERS.md) | Adapter internals | Claude in-process MCP approval server, Codex app-server JSON-RPC client, argv/JSON/method names, source-confirmed wire contracts |\\n34\\t| [docs/SYNC_PROTOCOL.md](docs/SYNC_PROTOCOL.md) | Mac ↔ iPhone | `ClientMsg`/`HostMsg`, `seq`-cursor catch-up, E2EE pairing (`SecureChannel`), first-responder approvals, verbosity throttling |\\n35\\t| [docs/WORKTREE_MANAGER.md](docs/WORKTREE_MANAGER.md) | Git | Worktree lifecycle, diff plumbing, merge/rebase/squash/PR + conflicts, crash reconciliation |\\n36\\t| [docs/RUNTIME_ARCHITECTURE.md](docs/RUNTIME_ARCHITECTURE.md) | Integration | Object graph, single-writer event pipeline, GRDB schema, approval bridging, Swift 6 concurrency |\\n37\\t| [docs/UX_MACOS.md](docs/UX_MACOS.md) | macOS UX | Navigation, dashboard, session detail, approval bar, create/approve/integrate flows |\\n38\\t| [docs/UX_IOS.md](docs/UX_IOS.md) | iPhone UX | Notification-first IA, approval flows, connectivity states, biometric gating |\\n39\\t| [docs/OBSERVABILITY_AND_TESTING.md](docs/OBSERVABILITY_AND_TESTING.md) | Cross-cutting | Local-first redaction-aware observability + hermetic test pyramid with fake-CLI fixtures |\\n40\\t\\n41\\t**The spine across all of them:** one normalized `AgentEvent` stream with a canonical monotonic\\n42\\t`seq`, written once by the `SessionController` (single writer), with the local transcript as the\\n43\\tsource of truth — UI, sync, and persistence are all subscribers. Every backend/transport\\n44\\tdifference is a declared *capability*, never an assumption. The single seam that unifies two very\\n45\\tdifferent approval mechanisms is `ApprovalCoordinator.await(...) -> Decision`.\\n46\\t\\n47\\t## Architecture\\n48\\t\\n49\\t```\\n50\\t┌───────────────────────── macOS host ─────────────────────────┐\\n51\\t│  SwiftUI app                                                  │\\n52\\t│  ┌──────────────┐   ┌────────────────────┐  ┌──────────────┐  │\\n53\\t│  │ Session UI   │   │ AgentBackend layer │  │ Git/Worktree │  │\\n54\\t│  │ (panes,diff, │◄─►│  ClaudeCodeBackend │  │   manager    │  │\\n55\\t│  │  approvals)  │   │  CodexBackend      │  └──────┬───────┘  │\\n56\\t│  └──────┬───────┘   └─────────┬──────────┘         │          │\\n57\\t│         │                     │ spawns + stream-json│         │\\n58\\t│         │            ┌────────▼────────┐    ┌───────▼───────┐ │\\n59\\t│         │            │ child processes │    │  git worktrees│ │\\n60\\t│         │            │ claude / codex  │    │  + branches   │ │\\n61\\t│         │            └─────────────────┘    └───────────────┘ │\\n62\\t│         │                                                     │\\n63\\t│  ┌──────▼──────────────── Sync server ──────────────────────┐ │\\n64\\t│  │  Network.framework (Bonjour/LAN)  +  relay client (later)│ │\\n65\\t│  └──────────────────────────┬──────────────────────────────┘ │\\n66\\t└─────────────────────────────┼────────────────────────────────┘\\n67\\t                              LAN  ╲  relay fallback (Cloudflare, later)\\n68\\t                               │    ╲\\n69\\t                        ┌──────▼─────────────┐\\n70\\t                        │   iPhone client     │\\n71\\t                        │ monitor + approve   │\\n72\\t                        └─────────────────────┘\\n73\\t```\\n74\\t\\n75\\t## Core domain model\\n76\\t\\n77\\tA small, backend-agnostic model everything else is built on.\\n78\\t\\n79\\t- **Project** — a registered git repo (root path, default branch, per-project config:\\n80\\t  setup script, approval defaults, default backend).\\n81\\t- **Session** — one agent run. Belongs to a Project, owns a **Worktree**, has a backend\\n82\\t  type, status (`idle / running / awaiting-approval / awaiting-input / finished / error`),\\n83\\t  and a transcript.\\n84\\t- **Worktree** — `path`, `branch`, base commit, dirty/clean, ahead/behind counts.\\n85\\t- **TranscriptEvent** — the normalized event stream (see backend section). Stored as JSONL\\n86\\t  on disk; metadata in the DB. **This local transcript is the UI's source of truth.**\\n87\\t- **ApprovalRequest** — tool name, input, risk, owning session; resolved with allow/deny\\n88\\t  (+ optional \\\"always for this tool/session\\\").\\n89\\t\\n90\\t## Pluggable agent backend (highest-leverage abstraction)\\n91\\t\\n92\\tOne protocol normalizes two genuinely different CLIs:\\n93\\t\\n94\\t```swift\\n95\\tprotocol AgentBackend {\\n96\\t    func start(in worktree: Worktree, prompt: String, opts: RunOptions) -> AsyncStream<AgentEvent>\\n97\\t    func send(_ input: AgentInput)          // follow-up turns\\n98\\t    func respond(to: ApprovalRequest, _ decision: Decision)\\n99\\t    func interrupt()\\n100\\t    func resume(sessionID: String) -> AsyncStream<AgentEvent>\\n101\\t}\\n102\\t```\\n103\\t\\n104\\t`AgentEvent` is a unified enum:\\n105\\t`.assistantText, .toolUse, .toolResult, .approvalRequest, .usage, .turnComplete, .error`.\\n106\\tEach backend translates its native output into it.\\n107\\t\\n108\\t- **ClaudeCodeBackend** — spawn\\n109\\t  `claude -p --output-format stream-json --input-format stream-json --verbose` and parse the\\n110\\t  JSONL events. For interactive approvals, register a tiny **in-process MCP \\\"approval\\\"\\n111\\t  server** and pass `--permission-prompt-tool`; Claude Code calls it on each gated tool, and\\n112\\t  we block that call until the UI resolves it. This is the supported way to get interactive\\n113\\t  per-session approvals from the CLI rather than scraping a TTY. Resume via\\n114\\t  `--resume <session_id>`.\\n115\\t- **CodexBackend** — spawn `codex` in its JSON/`exec` mode and map its approval/sandbox\\n116\\t  model onto the same `ApprovalRequest`. Codex's approval semantics differ (sandbox +\\n117\\t  ask-for-approval levels), so the adapter normalizes them — exactly why the protocol earns\\n118\\t  its keep.\\n119\\t\\n120\\tBuild **ClaudeCodeBackend first and fully**, then add Codex against the same protocol once\\n121\\tthe event/approval contract is proven.\\n122\\t\\n123\\t> The full event model, approval round-trip, capability matrix, and per-CLI adapter mappings\\n124\\t> are over-specified in [docs/BACKEND_PROTOCOL.md](docs/BACKEND_PROTOCOL.md). **Key finding:**\\n125\\t> Claude Code supports interactive approvals in headless mode, but Codex `exec` does not —\\n126\\t> interactive approvals require `codex app-server` (JSON-RPC), so that is the default Codex\\n127\\t> adapter. The protocol models this as a per-backend *capability*.\\n128\\t>\\n129\\t> Message-by-message adapter internals — the Claude in-process MCP approval server, the Codex\\n130\\t> app-server JSON-RPC client, argv/JSON examples, and a confidence-tagged validation backlog —\\n131\\t> are in [docs/ADAPTERS.md](docs/ADAPTERS.md). The single seam that unifies two very different\\n132\\t> approval mechanisms is `ApprovalCoordinator.await(...) -> Decision`.\\n133\\t\\n134\\t### Resume strategy\\n135\\t\\n136\\tUse each CLI's **native resume** (`--resume`/session files) to restart the agent's own\\n137\\tcontext, but treat **our local JSONL transcript as the UI source of truth** for rendering\\n138\\thistory. On resume we replay our transcript into the UI immediately and reattach the live\\n139\\tevent stream; we don't depend on the CLI to re-emit past turns. We can also import Claude\\n140\\tCode's own session files (`~/.claude/projects`) to bootstrap or recover.\\n141\\t\\n142\\t## Git / worktree manager\\n143\\t\\n144\\tThe Conductor-defining feature. Wraps `git` via subprocess (plain git over libgit2/SwiftGit2\\n145\\tfor simplicity and predictable behavior).\\n146\\t\\n147\\t- Create session → `git worktree add .nucleic/worktrees/<slug> -b nucleic/<slug>` off the\\n148\\t  chosen base.\\n149\\t- Run an optional **per-project setup script** in the new worktree (e.g. `npm install`)\\n150\\t  before the agent starts.\\n151\\t- Track diff vs base, ahead/behind, conflicts.\\n152\\t- Finish a session → review diff → **merge / rebase / squash back**, open a PR (`gh`), or\\n153\\t  discard. Clean up worktree + branch.\\n154\\t- Guardrails: worktree count limits, disk-usage checks, orphan cleanup on crash.\\n155\\t\\n156\\t> Fully specified in [docs/WORKTREE_MANAGER.md](docs/WORKTREE_MANAGER.md): the lifecycle\\n157\\t> state machine, exact diff plumbing (base-SHA anchor + working-tree capture so uncommitted\\n158\\t> agent work shows), finalize/integrate (merge/rebase/squash/PR) with conflict handling, and\\n159\\t> crash reconciliation against `git worktree list`.\\n160\\t\\n161\\t## macOS UI (SwiftUI)\\n162\\t\\n163\\t- **Sidebar**: projects → sessions, with live status badges.\\n164\\t- **Session detail**: transcript (assistant text, collapsible tool calls), a **live diff\\n165\\t  view**, log tail, and an inline **approval bar** when `awaiting-approval`.\\n166\\t- **New-session sheet**: pick project, base branch, backend (Claude/Codex), initial prompt.\\n167\\t- **Dashboard**: all running sessions at a glance — the \\\"10 agents at once\\\" view.\\n168\\t- Menu-bar item + native notifications when a session needs attention or finishes.\\n169\\t\\n170\\t> Information architecture, key screens (dashboard, session detail, approval bar), and the\\n171\\t> create/approve/integrate flows are wireframed in [docs/UX_MACOS.md](docs/UX_MACOS.md). The\\n172\\t> UI holds no canonical state — it observes the `SessionController` and sends intents, so Mac\\n173\\t> and iPhone are two renderers of the same authority.\\n174\\t\\n175\\t## Approvals flow (interactive, per-session)\\n176\\t\\n177\\tApproval originates in the backend (MCP approval tool for Claude; sandbox callback for\\n178\\tCodex) → becomes an `ApprovalRequest` → surfaced in the session UI **and** pushed to any\\n179\\tconnected iPhone → first responder wins → decision flows back and unblocks the agent.\\n180\\tSupport \\\"always allow this tool in this session\\\" to cut noise, persisted per-session. A\\n181\\tpre-configured policy layer can come later; the model already supports it.\\n182\\t\\n183\\t## Mac ↔ iPhone transport\\n184\\t\\n185\\t- **LAN (first)**: Bonjour + Network.framework (`NWListener`/`NWConnection`). Direct,\\n186\\t  low-latency when co-located. This is all v1 needs.\\n187\\t- **Relay fallback (later, on Cloudflare)**: a hosted WebSocket relay — a **Worker + Durable\\n188\\t  Object** per paired-device room (the DO holds connections and brokers messages).\\n189\\t- **Security**: device pairing (QR / code) and **end-to-end encryption** so the relay only\\n190\\t  ever sees ciphertext — it must never be able to read code or transcripts.\\n191\\t- **Protocol**: a small message set, identical over LAN and relay (only the transport swaps):\\n192\\t  `session.list`, `session.subscribe`, `event` (streamed transcript deltas),\\n193\\t  `approval.request` / `approval.respond`, `input.send`.\\n194\\t\\n195\\t> Fully specified in [docs/SYNC_PROTOCOL.md](docs/SYNC_PROTOCOL.md): the\\n196\\t> `ClientMsg`/`HostMsg` set, `seq`-cursor catch-up, first-responder-wins approvals,\\n197\\t> per-client verbosity throttling, and the pairing / E2EE (`SecureChannel`) design. The\\n198\\t> protocol is a projection of `AgentEvent` + the approval round-trip, and is\\n199\\t> transport-agnostic so LAN (v1) and the Cloudflare relay (later) share one message layer.\\n200\\t\\n201\\t## iPhone app\\n202\\t\\n203\\tSubscribes to the session list + live events, renders transcripts and diffs read-friendly,\\n204\\tand — the key interaction — **answers approval prompts** (push notifications via the relay,\\n205\\tonce relay exists) so you can unblock an agent from your phone. Mirrors a subset of the Mac\\n206\\tUI; no local git/CLI.\\n207\\t\\n208\\t> Information architecture, screens, and the notification-first approval flows are wireframed\\n209\\t> in [docs/UX_IOS.md](docs/UX_IOS.md). The phone is a pure projection of host state (scope\\n210\\t> `approve` in v1: view + approve + send follow-up input), is notification-first (Live\\n211\\t> Activity / widget / actionable pushes), gates risky approvals behind biometrics, and is\\n212\\t> explicit about connectivity (no optimistic actions; stale data is always labeled).\\n213\\t\\n214\\t## Persistence\\n215\\t\\n216\\t- **GRDB (SQLite)** for projects/sessions/approvals metadata — predictable, fast, good for a\\n217\\t  write-heavy event log. (SwiftData is the alternative.)\\n218\\t- **Transcripts as JSONL on disk** (mirrors how Claude Code stores sessions), referenced\\n219\\t  from the DB and serving as the UI source of truth.\\n220\\t\\n221\\t> The object graph, single-writer event pipeline, GRDB schema, approval bridging, resume\\n222\\t> wiring, and Swift 6 concurrency model are specified in\\n223\\t> [docs/RUNTIME_ARCHITECTURE.md](docs/RUNTIME_ARCHITECTURE.md). The `SessionController` actor\\n224\\t> is the single writer of each session's state; UI, sync, and DB all subscribe.\\n225\\t\\n226\\t## Observability & testing\\n227\\t\\n228\\t- **Local-first, redaction-aware observability**: OSLog with privacy specifiers (structural\\n229\\t  metadata public, content private), signpost tracing over the event pipeline, an in-app\\n230\\t  Diagnostics panel, and an opt-in per-session native-stream capture that doubles as a test\\n231\\t  fixture. An `unknown_events_total` counter is the CLI-drift early warning.\\n232\\t- **Hermetic test pyramid**: pure unit (golden event normalization, decision mapping, state\\n233\\t  machine, replay invariant) → component tests with a `FakeBackend` and real temp git repos →\\n234\\t  **adapter contract tests via fake CLI binaries** that speak the real wire protocols (no\\n235\\t  `claude`/`codex` needed) → opt-in nightly **live smoke** that re-records fixtures and emits a\\n236\\t  drift diff. Plus Noise/E2EE security tests and a Swift 6 strict-concurrency + TSAN gate.\\n237\\t\\n238\\t> Full design in [docs/OBSERVABILITY_AND_TESTING.md](docs/OBSERVABILITY_AND_TESTING.md). The\\n239\\t> core loop: a debugging capture today is a regression fixture tomorrow, and a CLI wire-format\\n240\\t> change trips the same drift signal from both the running app and nightly CI.\\n241\\t\\n242\\t## Tech stack\\n243\\t\\n244\\tSwift 6 + SwiftUI · `Network.framework` · `Foundation.Process` (or swift-subprocess) for\\n245\\tchild processes · GRDB · swift-async-algorithms for event streams · `git` / `gh` CLIs ·\\n246\\tCloudflare Worker + Durable Object relay (later).\\n247\\t\\n248\\t## Protocol validation status\\n249\\t\\n250\\tA source-validation pass (2026-06-11) resolved the load-bearing adapter unknowns against primary\\n251\\tsources, so M0 starts from confirmed contracts rather than guesses. Detail in\\n252\\t[docs/ADAPTERS.md](docs/ADAPTERS.md) §0.\\n253\\t\\n254\\t**Confirmed from source:**\\n255\\t- **Claude permission tool** (SDK docs \\\"Custom permission prompt tool\\\", archived 2025-05-31 +\\n256\\t  `@anthropic-ai/claude-agent-sdk` `sdk.d.ts`): tool receives `{tool_name, input, tool_use_id?}`;\\n257\\t  returns a **JSON-stringified** `{behavior:\\\"allow\\\",updatedInput}` / `{behavior:\\\"deny\\\",message}`\\n258\\t  inside an MCP text block — `behavior`/`message`, **not** `decision`/`reason`.\\n259\\t- **Codex app-server** (`openai/codex` source, commit `7a19b14`): real methods `initialize` →\\n260\\t  `thread/start` → `turn/start` → `turn/interrupt` / `thread/resume`; v2 approval decision enum\\n261\\t  `accept`/`acceptForSession`/`decline`/`cancel`; streaming deltas + `turn/steer` exist; token\\n262\\t  usage via separate `thread/tokenUsage/updated`.\\n263\\t- **Codex exec** (`codex-rs/exec/src/exec_events.rs`, rust-v0.139.0): a **distinct snake_case\\n264\\t  schema** from app-server's camelCase → needs its own decoder; usage inline on `turn.completed`.\\n265\\t\\n266\\t**Residual (needs a live capture in M0, not docs):** Claude's stdin user-message envelope, the\\n267\\t`thinking` block + `stream_event` partial shapes, verbatim golden sample lines for both CLIs, and\\n268\\tCodex exec's exact fail-closed behavior on a gated action. These are precisely what the M0\\n269\\tfixtures harness produces.\\n270\\t\\n271\\t**M0 capture pass (2026-06-12):** all Claude-side residuals are now pinned against the real CLI\\n272\\t(2.1.167) — stdin envelope, `thinking`/`stream_event` shapes, and the full approval round-trip,\\n273\\tplus one critical finding: the adapter must pass `--permission-mode default` or the host's\\n274\\tuser-level `defaultMode` (e.g. `\\\"auto\\\"`) silently bypasses the permission tool. Golden captures\\n275\\tlive in `fixtures/claude/2.1.167/`. Details in [docs/M0_RESULTS.md](docs/M0_RESULTS.md).\\n276\\tCodex-side residuals remain (no `codex` on the dev machine; M3).\\n277\\t\\n278\\t## Milestones\\n279\\t\\n280\\t1. **M0 — Spike** ✅ *(done 2026-06-12)*: spawn `claude` in stream-json, parse events into\\n281\\t   `AgentEvent`, print to console. Prove the event contract; capture the residual fixtures\\n282\\t   above. Shipped as the `NucleicCore` package + `nucleic-spike` CLI + `fake-claude` test\\n283\\t   stub with 41 hermetic tests — see [docs/M0_RESULTS.md](docs/M0_RESULTS.md).\\n284\\t2. **M1 — Single-session macOS MVP**: one project, create worktree, run a Claude session,\\n285\\t   transcript + diff + interactive approvals, merge/discard back.\\n286\\t3. **M2 — Parallel + dashboard**: many concurrent sessions, status badges, the\\n287\\t   \\\"agents at once\\\" view, robust cleanup.\\n288\\t4. **M3 — Codex backend**: second backend against the same protocol; backend picker.\\n289\\t5. **M4 — iPhone over LAN**: sync server + Bonjour, iOS client monitors + approves on the\\n290\\t   same network.\\n291\\t6. **M5 — Cloudflare relay + notifications**: Worker/DO relay, E2EE pairing, APNs approvals\\n292\\t   from anywhere.\\n293\\t7. **M6 — Polish**: per-project setup scripts, PR creation, policy approvals, usage/cost\\n294\\t   display, then revisit **distribution** (signing / notarization / MAS).\\n295\\t\\n296\\t## Deferred / revisit later\\n297\\t\\n298\\t- **Distribution** — signing, notarization, and whether to ship outside the Mac App Store\\n299\\t  (App Sandbox is likely impractical given arbitrary subprocess + repo access). Decide near\\n300\\t  M6.\\n301\\t- **Cloud relay** — built on Cloudflare, but only after LAN sync (M4) is solid.\\n302\\t\"}]},\"parent_tool_use_id\":null,\"session_id\":\"c29d82c3-3baa-4f88-b8d1-04151486ebe4\",\"uuid\":\"e18ffbd3-430d-4a99-b0cc-3858f0794143\",\"timestamp\":\"2026-06-12T23:34:29.724Z\",\"tool_use_result\":{\"type\":\"text\",\"file\":{\"filePath\":\"/Users/blakeslee/Library/Mobile Documents/com~apple~CloudDocs/projects/nucleic/.claude/worktrees/laughing-buck-c3b99c/PLAN.md\",\"content\":\"# Nucleic — Plan\\n\\nA macOS app (codename **Nucleic**) that runs multiple Claude Code / Codex sessions in\\nparallel, each isolated in its own git worktree + branch, with a SwiftUI cockpit to start,\\nwatch, approve, and merge them. A companion iPhone app connects to the Mac as a remote\\nclient to monitor sessions and answer approval prompts on the go.\\n\\nThe Mac is the **host** (does all real work: spawns CLIs, owns the repos). The iPhone is a\\n**thin remote client**. This host/client split is the spine of the whole design.\\n\\n## Locked decisions\\n\\n| Decision | Choice |\\n| --- | --- |\\n| Agents wrapped | Both Claude Code + Codex, behind one pluggable backend protocol |\\n| Concurrency model | Parallel git worktrees (the defining feature) |\\n| Agent integration | Wrap the CLI as a subprocess; parse `stream-json` output |\\n| Platforms | macOS (host) + iPhone (remote client) |\\n| iPhone role | Remote client to the Mac (monitor + approve) |\\n| Mac ↔ iPhone transport | LAN first; cloud relay fallback added later |\\n| Approvals | Interactive, per-session |\\n| Session resume | **Native CLI resume + a local transcript as the UI source of truth** |\\n| Distribution | **Deferred** — decide signing/notarization/MAS later |\\n| Relay hosting | **Build on Cloudflare, but later** — LAN-only for the first usable version |\\n\\n## Document set\\n\\nThis file is the hub and overview. Each layer is over-specified in its own doc:\\n\\n| Doc | Layer | Locks down |\\n| --- | --- | --- |\\n| [docs/BACKEND_PROTOCOL.md](docs/BACKEND_PROTOCOL.md) | Agent abstraction | `AgentBackend`, the normalized `AgentEvent` model, capability matrix, approval round-trip, per-CLI adapter mappings |\\n| [docs/ADAPTERS.md](docs/ADAPTERS.md) | Adapter internals | Claude in-process MCP approval server, Codex app-server JSON-RPC client, argv/JSON/method names, source-confirmed wire contracts |\\n| [docs/SYNC_PROTOCOL.md](docs/SYNC_PROTOCOL.md) | Mac ↔ iPhone | `ClientMsg`/`HostMsg`, `seq`-cursor catch-up, E2EE pairing (`SecureChannel`), first-responder approvals, verbosity throttling |\\n| [docs/WORKTREE_MANAGER.md](docs/WORKTREE_MANAGER.md) | Git | Worktree lifecycle, diff plumbing, merge/rebase/squash/PR + conflicts, crash reconciliation |\\n| [docs/RUNTIME_ARCHITECTURE.md](docs/RUNTIME_ARCHITECTURE.md) | Integration | Object graph, single-writer event pipeline, GRDB schema, approval bridging, Swift 6 concurrency |\\n| [docs/UX_MACOS.md](docs/UX_MACOS.md) | macOS UX | Navigation, dashboard, session detail, approval bar, create/approve/integrate flows |\\n| [docs/UX_IOS.md](docs/UX_IOS.md) | iPhone UX | Notification-first IA, approval flows, connectivity states, biometric gating |\\n| [docs/OBSERVABILITY_AND_TESTING.md](docs/OBSERVABILITY_AND_TESTING.md) | Cross-cutting | Local-first redaction-aware observability + hermetic test pyramid with fake-CLI fixtures |\\n\\n**The spine across all of them:** one normalized `AgentEvent` stream with a canonical monotonic\\n`seq`, written once by the `SessionController` (single writer), with the local transcript as the\\nsource of truth — UI, sync, and persistence are all subscribers. Every backend/transport\\ndifference is a declared *capability*, never an assumption. The single seam that unifies two very\\ndifferent approval mechanisms is `ApprovalCoordinator.await(...) -> Decision`.\\n\\n## Architecture\\n\\n```\\n┌───────────────────────── macOS host ─────────────────────────┐\\n│  SwiftUI app                                                  │\\n│  ┌──────────────┐   ┌────────────────────┐  ┌──────────────┐  │\\n│  │ Session UI   │   │ AgentBackend layer │  │ Git/Worktree │  │\\n│  │ (panes,diff, │◄─►│  ClaudeCodeBackend │  │   manager    │  │\\n│  │  approvals)  │   │  CodexBackend      │  └──────┬───────┘  │\\n│  └──────┬───────┘   └─────────┬──────────┘         │          │\\n│         │                     │ spawns + stream-json│         │\\n│         │            ┌────────▼────────┐    ┌───────▼───────┐ │\\n│         │            │ child processes │    │  git worktrees│ │\\n│         │            │ claude / codex  │    │  + branches   │ │\\n│         │            └─────────────────┘    └───────────────┘ │\\n│         │                                                     │\\n│  ┌──────▼──────────────── Sync server ──────────────────────┐ │\\n│  │  Network.framework (Bonjour/LAN)  +  relay client (later)│ │\\n│  └──────────────────────────┬──────────────────────────────┘ │\\n└─────────────────────────────┼────────────────────────────────┘\\n                              LAN  ╲  relay fallback (Cloudflare, later)\\n                               │    ╲\\n                        ┌──────▼─────────────┐\\n                        │   iPhone client     │\\n                        │ monitor + approve   │\\n                        └─────────────────────┘\\n```\\n\\n## Core domain model\\n\\nA small, backend-agnostic model everything else is built on.\\n\\n- **Project** — a registered git repo (root path, default branch, per-project config:\\n  setup script, approval defaults, default backend).\\n- **Session** — one agent run. Belongs to a Project, owns a **Worktree**, has a backend\\n  type, status (`idle / running / awaiting-approval / awaiting-input / finished / error`),\\n  and a transcript.\\n- **Worktree** — `path`, `branch`, base commit, dirty/clean, ahead/behind counts.\\n- **TranscriptEvent** — the normalized event stream (see backend section). Stored as JSONL\\n  on disk; metadata in the DB. **This local transcript is the UI's source of truth.**\\n- **ApprovalRequest** — tool name, input, risk, owning session; resolved with allow/deny\\n  (+ optional \\\"always for this tool/session\\\").\\n\\n## Pluggable agent backend (highest-leverage abstraction)\\n\\nOne protocol normalizes two genuinely different CLIs:\\n\\n```swift\\nprotocol AgentBackend {\\n    func start(in worktree: Worktree, prompt: String, opts: RunOptions) -> AsyncStream<AgentEvent>\\n    func send(_ input: AgentInput)          // follow-up turns\\n    func respond(to: ApprovalRequest, _ decision: Decision)\\n    func interrupt()\\n    func resume(sessionID: String) -> AsyncStream<AgentEvent>\\n}\\n```\\n\\n`AgentEvent` is a unified enum:\\n`.assistantText, .toolUse, .toolResult, .approvalRequest, .usage, .turnComplete, .error`.\\nEach backend translates its native output into it.\\n\\n- **ClaudeCodeBackend** — spawn\\n  `claude -p --output-format stream-json --input-format stream-json --verbose` and parse the\\n  JSONL events. For interactive approvals, register a tiny **in-process MCP \\\"approval\\\"\\n  server** and pass `--permission-prompt-tool`; Claude Code calls it on each gated tool, and\\n  we block that call until the UI resolves it. This is the supported way to get interactive\\n  per-session approvals from the CLI rather than scraping a TTY. Resume via\\n  `--resume <session_id>`.\\n- **CodexBackend** — spawn `codex` in its JSON/`exec` mode and map its approval/sandbox\\n  model onto the same `ApprovalRequest`. Codex's approval semantics differ (sandbox +\\n  ask-for-approval levels), so the adapter normalizes them — exactly why the protocol earns\\n  its keep.\\n\\nBuild **ClaudeCodeBackend first and fully**, then add Codex against the same protocol once\\nthe event/approval contract is proven.\\n\\n> The full event model, approval round-trip, capability matrix, and per-CLI adapter mappings\\n> are over-specified in [docs/BACKEND_PROTOCOL.md](docs/BACKEND_PROTOCOL.md). **Key finding:**\\n> Claude Code supports interactive approvals in headless mode, but Codex `exec` does not —\\n> interactive approvals require `codex app-server` (JSON-RPC), so that is the default Codex\\n> adapter. The protocol models this as a per-backend *capability*.\\n>\\n> Message-by-message adapter internals — the Claude in-process MCP approval server, the Codex\\n> app-server JSON-RPC client, argv/JSON examples, and a confidence-tagged validation backlog —\\n> are in [docs/ADAPTERS.md](docs/ADAPTERS.md). The single seam that unifies two very different\\n> approval mechanisms is `ApprovalCoordinator.await(...) -> Decision`.\\n\\n### Resume strategy\\n\\nUse each CLI's **native resume** (`--resume`/session files) to restart the agent's own\\ncontext, but treat **our local JSONL transcript as the UI source of truth** for rendering\\nhistory. On resume we replay our transcript into the UI immediately and reattach the live\\nevent stream; we don't depend on the CLI to re-emit past turns. We can also import Claude\\nCode's own session files (`~/.claude/projects`) to bootstrap or recover.\\n\\n## Git / worktree manager\\n\\nThe Conductor-defining feature. Wraps `git` via subprocess (plain git over libgit2/SwiftGit2\\nfor simplicity and predictable behavior).\\n\\n- Create session → `git worktree add .nucleic/worktrees/<slug> -b nucleic/<slug>` off the\\n  chosen base.\\n- Run an optional **per-project setup script** in the new worktree (e.g. `npm install`)\\n  before the agent starts.\\n- Track diff vs base, ahead/behind, conflicts.\\n- Finish a session → review diff → **merge / rebase / squash back**, open a PR (`gh`), or\\n  discard. Clean up worktree + branch.\\n- Guardrails: worktree count limits, disk-usage checks, orphan cleanup on crash.\\n\\n> Fully specified in [docs/WORKTREE_MANAGER.md](docs/WORKTREE_MANAGER.md): the lifecycle\\n> state machine, exact diff plumbing (base-SHA anchor + working-tree capture so uncommitted\\n> agent work shows), finalize/integrate (merge/rebase/squash/PR) with conflict handling, and\\n> crash reconciliation against `git worktree list`.\\n\\n## macOS UI (SwiftUI)\\n\\n- **Sidebar**: projects → sessions, with live status badges.\\n- **Session detail**: transcript (assistant text, collapsible tool calls), a **live diff\\n  view**, log tail, and an inline **approval bar** when `awaiting-approval`.\\n- **New-session sheet**: pick project, base branch, backend (Claude/Codex), initial prompt.\\n- **Dashboard**: all running sessions at a glance — the \\\"10 agents at once\\\" view.\\n- Menu-bar item + native notifications when a session needs attention or finishes.\\n\\n> Information architecture, key screens (dashboard, session detail, approval bar), and the\\n> create/approve/integrate flows are wireframed in [docs/UX_MACOS.md](docs/UX_MACOS.md). The\\n> UI holds no canonical state — it observes the `SessionController` and sends intents, so Mac\\n> and iPhone are two renderers of the same authority.\\n\\n## Approvals flow (interactive, per-session)\\n\\nApproval originates in the backend (MCP approval tool for Claude; sandbox callback for\\nCodex) → becomes an `ApprovalRequest` → surfaced in the session UI **and** pushed to any\\nconnected iPhone → first responder wins → decision flows back and unblocks the agent.\\nSupport \\\"always allow this tool in this session\\\" to cut noise, persisted per-session. A\\npre-configured policy layer can come later; the model already supports it.\\n\\n## Mac ↔ iPhone transport\\n\\n- **LAN (first)**: Bonjour + Network.framework (`NWListener`/`NWConnection`). Direct,\\n  low-latency when co-located. This is all v1 needs.\\n- **Relay fallback (later, on Cloudflare)**: a hosted WebSocket relay — a **Worker + Durable\\n  Object** per paired-device room (the DO holds connections and brokers messages).\\n- **Security**: device pairing (QR / code) and **end-to-end encryption** so the relay only\\n  ever sees ciphertext — it must never be able to read code or transcripts.\\n- **Protocol**: a small message set, identical over LAN and relay (only the transport swaps):\\n  `session.list`, `session.subscribe`, `event` (streamed transcript deltas),\\n  `approval.request` / `approval.respond`, `input.send`.\\n\\n> Fully specified in [docs/SYNC_PROTOCOL.md](docs/SYNC_PROTOCOL.md): the\\n> `ClientMsg`/`HostMsg` set, `seq`-cursor catch-up, first-responder-wins approvals,\\n> per-client verbosity throttling, and the pairing / E2EE (`SecureChannel`) design. The\\n> protocol is a projection of `AgentEvent` + the approval round-trip, and is\\n> transport-agnostic so LAN (v1) and the Cloudflare relay (later) share one message layer.\\n\\n## iPhone app\\n\\nSubscribes to the session list + live events, renders transcripts and diffs read-friendly,\\nand — the key interaction — **answers approval prompts** (push notifications via the relay,\\nonce relay exists) so you can unblock an agent from your phone. Mirrors a subset of the Mac\\nUI; no local git/CLI.\\n\\n> Information architecture, screens, and the notification-first approval flows are wireframed\\n> in [docs/UX_IOS.md](docs/UX_IOS.md). The phone is a pure projection of host state (scope\\n> `approve` in v1: view + approve + send follow-up input), is notification-first (Live\\n> Activity / widget / actionable pushes), gates risky approvals behind biometrics, and is\\n> explicit about connectivity (no optimistic actions; stale data is always labeled).\\n\\n## Persistence\\n\\n- **GRDB (SQLite)** for projects/sessions/approvals metadata — predictable, fast, good for a\\n  write-heavy event log. (SwiftData is the alternative.)\\n- **Transcripts as JSONL on disk** (mirrors how Claude Code stores sessions), referenced\\n  from the DB and serving as the UI source of truth.\\n\\n> The object graph, single-writer event pipeline, GRDB schema, approval bridging, resume\\n> wiring, and Swift 6 concurrency model are specified in\\n> [docs/RUNTIME_ARCHITECTURE.md](docs/RUNTIME_ARCHITECTURE.md). The `SessionController` actor\\n> is the single writer of each session's state; UI, sync, and DB all subscribe.\\n\\n## Observability & testing\\n\\n- **Local-first, redaction-aware observability**: OSLog with privacy specifiers (structural\\n  metadata public, content private), signpost tracing over the event pipeline, an in-app\\n  Diagnostics panel, and an opt-in per-session native-stream capture that doubles as a test\\n  fixture. An `unknown_events_total` counter is the CLI-drift early warning.\\n- **Hermetic test pyramid**: pure unit (golden event normalization, decision mapping, state\\n  machine, replay invariant) → component tests with a `FakeBackend` and real temp git repos →\\n  **adapter contract tests via fake CLI binaries** that speak the real wire protocols (no\\n  `claude`/`codex` needed) → opt-in nightly **live smoke** that re-records fixtures and emits a\\n  drift diff. Plus Noise/E2EE security tests and a Swift 6 strict-concurrency + TSAN gate.\\n\\n> Full design in [docs/OBSERVABILITY_AND_TESTING.md](docs/OBSERVABILITY_AND_TESTING.md). The\\n> core loop: a debugging capture today is a regression fixture tomorrow, and a CLI wire-format\\n> change trips the same drift signal from both the running app and nightly CI.\\n\\n## Tech stack\\n\\nSwift 6 + SwiftUI · `Network.framework` · `Foundation.Process` (or swift-subprocess) for\\nchild processes · GRDB · swift-async-algorithms for event streams · `git` / `gh` CLIs ·\\nCloudflare Worker + Durable Object relay (later).\\n\\n## Protocol validation status\\n\\nA source-validation pass (2026-06-11) resolved the load-bearing adapter unknowns against primary\\nsources, so M0 starts from confirmed contracts rather than guesses. Detail in\\n[docs/ADAPTERS.md](docs/ADAPTERS.md) §0.\\n\\n**Confirmed from source:**\\n- **Claude permission tool** (SDK docs \\\"Custom permission prompt tool\\\", archived 2025-05-31 +\\n  `@anthropic-ai/claude-agent-sdk` `sdk.d.ts`): tool receives `{tool_name, input, tool_use_id?}`;\\n  returns a **JSON-stringified** `{behavior:\\\"allow\\\",updatedInput}` / `{behavior:\\\"deny\\\",message}`\\n  inside an MCP text block — `behavior`/`message`, **not** `decision`/`r","type":"raw"},"seq":65,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
{"at":"2026-06-12T23:34:40Z","backend":"claudeCode","kind":{"outcome":"completed","type":"runFinished"},"seq":66,"sessionID":"5C9CD482-73AC-4470-B3E1-F336DD8F4D38"}
```
