docs: update meta files for S-1 Phase 3 worktree isolation

.claude/CLAUDE.md

@@ -35,7 +35,8 @@
 - Sidecar uses per-provider runner bundles (`sidecar/dist/{provider}-runner.mjs`). Currently only `claude-runner.mjs` exists. SidecarManager.resolve_sidecar_for_provider(provider) finds the right runner file. Deno preferred (faster startup), Node.js fallback. Communicates with Rust via stdio NDJSON. Claude CLI auto-detected at startup via `findClaudeCli()` — checks ~/.local/bin/claude, ~/.claude/local/claude, /usr/local/bin/claude, /usr/bin/claude, then `which claude`. Path passed to SDK via `pathToClaudeCodeExecutable` option. Agents error immediately if CLI not found. Provider env var stripping: strip_provider_env_var() strips CLAUDE*/CODEX*/OLLAMA* vars (whitelists CLAUDE_CODE_EXPERIMENTAL_*). Dual-layer: (1) Rust env_clear() + clean_env, (2) JS runner SDK `env` option. Session stop uses AbortController.abort(). `agent-runner-deno.ts` exists as standalone alternative runner but is NOT used by SidecarManager.
 - AgentPane does NOT stop agents in onDestroy — onDestroy fires on layout remounts, not just explicit close. Stop-on-close is handled externally (was TilingGrid in v2, now workspace teardown in v3).
 - Agent dispatcher (`src/lib/agent-dispatcher.ts`) is a singleton that routes sidecar events to the agent store. Provider-aware: sessionProviderMap routes messages through adaptMessage(provider, event) from message-adapters.ts. Handles subagent routing (project-scoped sessions skip layout pane, render in TeamAgentsPanel; detached mode creates layout pane). Session persistence via registerSessionProject(sessionId, projectId, provider) + persistSessionForProject() (saves state + messages to SQLite on complete).
-- AgentQueryOptions supports `provider` field (defaults to 'claude', flows Rust -> sidecar), `provider_config` blob (Rust passes through as serde_json::Value), `permission_mode` (defaults to 'bypassPermissions'), `setting_sources` (defaults to ['user', 'project']), `system_prompt`, `model`, `claude_config_dir` (for multi-account), `additional_directories`.
+- AgentQueryOptions supports `provider` field (defaults to 'claude', flows Rust -> sidecar), `provider_config` blob (Rust passes through as serde_json::Value), `permission_mode` (defaults to 'bypassPermissions'), `setting_sources` (defaults to ['user', 'project']), `system_prompt`, `model`, `claude_config_dir` (for multi-account), `additional_directories`, `worktree_name` (when set, passed as `extraArgs: { worktree: name }` to SDK → `--worktree <name>` CLI flag).
+- Worktree isolation (S-1 Phase 3): Per-project `useWorktrees` toggle in SettingsTab. When enabled, AgentPane passes `worktree_name=sessionId` in queryAgent(). Agent runs in `<repo>/.claude/worktrees/<sessionId>/`. CWD-based detection: agent-dispatcher.ts `detectWorktreeFromCwd()` matches `.claude/worktrees/`, `.codex/worktrees/`, `.cursor/worktrees/` patterns on init events → calls `setSessionWorktree()` for conflict suppression. Dual detection: CWD-based (primary, from init event) + tool_call-based `extractWorktreePath()` (subagent fallback).
 - Claude profiles: claude_list_profiles() reads ~/.config/switcher/profiles/ with profile.toml metadata. Profile set per-project in Settings (project.profile field), passed through AgentSession -> AgentPane `profile` prop -> resolved to config_dir for SDK. Profile name shown as info-only in ProjectHeader.
 - ProjectBox has project-level tab bar: Model | Docs | Context | Files | SSH | Memory. Three mount strategies: PERSISTED-EAGER (Model, Docs, Context — always mounted, display:flex/none), PERSISTED-LAZY (Files, SSH, Memory — mount on first activation via {#if everActivated} + display:flex/none). Tab type: `'model' | 'docs' | 'context' | 'files' | 'ssh' | 'memories'`. Model tab = AgentSession+TeamAgentsPanel. Docs tab = ProjectFiles (markdown viewer). Context tab = ContextTab.svelte (LLM context window visualization: stats bar, segmented token meter, file references, turn breakdown; reads from agent store via sessionId prop; replaced old ContextPane ctx database viewer). Files tab = FilesTab.svelte (VSCode-style directory tree + CodeMirror 6 editor with 15 language modes, dirty tracking, Ctrl+S save, save-on-blur setting, image display via convertFileSrc, 10MB gate; CodeEditor.svelte wrapper; PdfViewer.svelte for PDF files via pdfjs-dist with canvas multi-page rendering + zoom 0.5x–3x; CsvTable.svelte for CSV with RFC 4180 parser, delimiter auto-detect, sortable columns). SSH tab = SshTab.svelte (CRUD for SSH connections, launch spawns terminal tab in Model tab). Memory tab = MemoriesTab.svelte (pluggable via MemoryAdapter interface in memory-adapter.ts). Rust backend: list_directory_children + read_file_content + write_file_content (FileContent tagged union: Text/Binary/TooLarge). Frontend bridge: files-bridge.ts.
 - ProjectHeader shows CWD (ellipsized from START via `direction: rtl`) + profile name as info-only text on right side. AgentPane no longer has DIR/ACC toolbar — CWD and profile are props from parent.

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `claude_read_skill` path traversal: added `canonicalize()` + `starts_with()` validation to prevent reading arbitrary files via crafted skill paths (lib.rs)
 
 ### Added
+- **S-1 Phase 3: Worktree isolation per project** — per-project `useWorktrees` toggle in SettingsTab. When enabled, agents run in git worktrees at `<repo>/.claude/worktrees/<sessionId>/` via SDK `extraArgs: { worktree: sessionId }`. CWD-based worktree detection in agent-dispatcher (`detectWorktreeFromCwd()`) matches `.claude/`, `.codex/`, `.cursor/` worktree patterns on init events. Dual detection: CWD-based (primary) + tool_call-based (subagent fallback). 8 files, +125 lines, 7 new tests. 226 vitest + 42 cargo tests
 - **S-2 Session Anchors** — preserves important conversation turns through context compaction chains. Auto-anchors first 3 turns with observation masking (reasoning preserved in full per research). Manual pin button on AgentPane text messages. Three anchor types: auto (re-injectable), pinned (display-only), promoted (user-promoted, re-injectable). Re-injection via `system_prompt` field. ContextTab anchor section with budget meter bar, per-anchor promote/demote/remove actions. SQLite `session_anchors` table with 5 CRUD commands. 5 new files, 7 modified. 219 vitest + 42 cargo tests
 - **Configurable anchor budget scale** — `AnchorBudgetScale` type with 4 presets: Small (2K), Medium (6K, default), Large (12K), Full (20K). Per-project 4-stop range slider in SettingsTab. `ProjectConfig.anchorBudgetScale` persisted in groups.json. ContextTab budget meter derives from project setting. agent-dispatcher resolves scale on auto-anchor
 - **Agent provider adapter pattern** — full implementation (3 phases complete): core abstraction layer (provider types/registry/capabilities, message adapter registry, 4 file renames), Settings UI (collapsible per-provider config panels, per-project provider dropdown, settings persistence), sidecar routing (provider-based runner selection, env var stripping for CLAUDE*/CODEX*/OLLAMA*). 5 new files, 4 renames, 20+ modified. 6 architecture decisions (PA-1–PA-6). Docs at `docs/provider-adapter/`

CLAUDE.md

@@ -58,7 +58,7 @@ Terminal emulator with SSH and Claude Code session management. v1 (GTK3+VTE Pyth
 | `v2/src/lib/providers/types.ts` | Provider abstraction types (ProviderId, ProviderCapabilities, ProviderMeta, ProviderSettings) |
 | `v2/src/lib/providers/registry.svelte.ts` | Svelte 5 rune-based provider registry (registerProvider, getProviders) |
 | `v2/src/lib/providers/claude.ts` | Claude provider metadata constant (CLAUDE_PROVIDER) |
-| `v2/src/lib/agent-dispatcher.ts` | Routes sidecar events to agent store + subagent routing + session persistence + toast notifications |
+| `v2/src/lib/agent-dispatcher.ts` | Routes sidecar events to agent store + subagent routing + session persistence + toast notifications + CWD-based worktree detection |
 | `v2/src/lib/adapters/file-bridge.ts` | File watcher IPC wrapper |
 | `v2/src/lib/adapters/settings-bridge.ts` | Settings IPC wrapper (get/set/list) |
 | `v2/src/lib/adapters/ctx-bridge.ts` | ctx database IPC wrapper |

TODO.md

@@ -10,10 +10,10 @@
 - [ ] **Agent Teams real-world testing** -- Env var whitelist fix done. 3 test sessions ran ($1.10, $0.69, $1.70) but model didn't spawn subagents — needs complex multi-part prompts to trigger delegation. Test with CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS=1.
 - [ ] **Configurable stall threshold** -- health.yaml per-project config for stall threshold (currently hardcoded 15 min). Adaptive suggestions after 50 sessions from session_metrics data.
 - [ ] **Add Codex/Ollama provider runners** -- Provider adapter pattern implemented (all 3 phases). Need to create codex-runner.ts and ollama-runner.ts sidecar runners + corresponding message adapters (codex-messages.ts, ollama-messages.ts) + register providers in App.svelte.
-- [ ] **Worktree isolation per project (S-1 Phase 3)** -- Three parts: (1) **UI toggle**: useWorktrees checkbox in SettingsTab per-project settings, persisted in groups.json ProjectConfig. (2) **Spawn with --worktree**: when useWorktrees=true, pass `--worktree <session-slug>` flag to Claude Code CLI via sidecar AgentQueryOptions. Sidecar creates worktree at `<cwd>/.claude/worktrees/<name>/`, agent CWD is set there. (3) **Worktree detection improvement**: current extractWorktreePath checks tool_call params, but agents don't signal worktrees in tool calls — the real signal is CWD-based (path contains `.claude/worktrees/`) or from sidecar notification events (`worktreePath`/`worktreeBranch` fields, Claude Code v2.1.72+). Update agent-dispatcher to parse init event CWD or notification fields. For Codex/Cursor agents: detect `$CODEX_HOME/worktrees/` or `~/.cursor/worktrees/` CWD patterns. Conflict suppression already works once worktree is registered via setSessionWorktree().
 
 ## Completed
 
+- [x] **Worktree isolation per project (S-1 Phase 3)** -- UI toggle in SettingsTab, spawn with --worktree via sidecar extraArgs, CWD-based worktree detection in agent-dispatcher (matches .claude/.codex/.cursor patterns). 8 files, +125 lines. 226 vitest + 42 cargo tests. | Done: 2026-03-11
 - [x] **S-2 — Session Anchors + Configurable Budget** -- Preserves important turns through compaction chains. Auto-anchors first 3 turns (observation-masked — reasoning preserved in full per research). Configurable budget via AnchorBudgetScale slider (Small=2K, Medium=6K, Large=12K, Full=20K) in SettingsTab per-project. Manual pin, promote/demote in ContextTab. Re-injection via system_prompt. 219 vitest + 42 cargo tests. | Done: 2026-03-11
 - [x] **Agent provider adapter pattern** -- Multi-provider support (Claude, Codex, Ollama) via 3-phase adapter pattern. Core abstraction, Settings UI, Sidecar routing. 5 new files, 4 renames, 20+ modified. 202 vitest + 42 cargo tests. | Done: 2026-03-11
 - [x] **Files tab PDF viewer + CSV table** -- PdfViewer.svelte (pdfjs-dist 5.5.207, canvas multi-page, zoom 0.5x–3x, HiDPI). CsvTable.svelte (RFC 4180 parser, delimiter auto-detect, sortable columns, sticky header). | Done: 2026-03-11
@@ -23,4 +23,3 @@
 - [x] **Project Health Dashboard (S-3)** -- health.svelte.ts store, Mission Control status bar, session_metrics SQLite table. | Done: 2026-03-10
 - [x] **Context tab repurpose** -- Replaced ContextPane with ContextTab (LLM context window visualization). | Done: 2026-03-10
 - [x] **CodeMirror 6 editor** -- Replaced shiki viewer with CodeMirror 6. 15 language modes, Catppuccin theme. | Done: 2026-03-10
-- [x] **FilesTab reactivity fixes** -- Fixed HTML nesting, Svelte 5 $state proxy reactivity. | Done: 2026-03-10

docs/v3-progress.md

@@ -637,3 +637,28 @@ All editor themes map to the same `--ctp-*` CSS custom property names (26 vars).
 #### Verification
 - [x] vitest: 219/219 tests pass (no regressions)
 - [x] cargo test: 42/42 pass (no regressions)
+
+### Session: 2026-03-11 — S-1 Phase 3: Worktree Isolation Per Project
+
+#### UI toggle
+- [x] Added 'Worktree Isolation' checkbox to SettingsTab per-project card (card-field-row CSS layout)
+- [x] ProjectConfig.useWorktrees? already existed — wired to toggle
+
+#### Spawn with worktree flag
+- [x] Added worktree_name: Option<String> to AgentQueryOptions (Rust sidecar.rs)
+- [x] Added worktree_name?: string to TS AgentQueryOptions (agent-bridge.ts)
+- [x] Sidecar JSON passes worktreeName field to claude-runner.ts
+- [x] claude-runner.ts passes extraArgs: { worktree: name } to SDK query() (maps to --worktree CLI flag)
+- [x] AgentPane: added useWorktrees prop, passes worktree_name=sessionId when enabled
+- [x] AgentSession: passes useWorktrees={project.useWorktrees} to AgentPane
+- [x] Rebuilt sidecar bundle (claude-runner.mjs)
+
+#### CWD-based worktree detection
+- [x] Added detectWorktreeFromCwd() to agent-dispatcher.ts (matches .claude/.codex/.cursor worktree patterns)
+- [x] Init event handler now calls setSessionWorktree() when CWD contains worktree path
+- [x] Dual detection: CWD-based (primary) + tool_call-based extractWorktreePath (subagent fallback)
+
+#### Tests
+- [x] Added 7 new tests to agent-dispatcher.test.ts (detectWorktreeFromCwd unit tests + init CWD integration)
+- [x] vitest: 226/226 tests pass
+- [x] cargo test: 42/42 pass