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MCP tools require permission by default. Add mcp__* to allowedTools
when MCPs are configured and we're in research phase, since that's
where external data sources are most useful.
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- Add McpSettings component with add/edit/delete server UI
- Support stdio (command + args + env) and sse/http (url + headers) transports
- Array builder for args, key-value builder for env vars and headers
- Pass mcpServers config to SDK query() calls
- Store config as JSON in settings table
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- Add Model settings section with free-text input for model override
- Pass configured model through to SDK query() calls
- Display active model badge in ActionBar next to token usage
- Seed model state from DB on mount, update from system:init events
- Empty/unset value uses SDK default (no breaking change)
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- ✅ **1. `src/main/db/schema.ts`** — add `settings` table to `initSchema`
- ✅ **2. `src/main/db/settings.ts`** — create file with `getSetting`, `getSettings`, `setSetting`, `deleteSetting`
- ✅ **3. `src/main/claude/phases.ts`** — add `customSystemPrompt?` param to `getPhaseConfig`; add `getDefaultSystemPromptTemplate` export
- ✅ **4. `src/main/claude/index.ts`** — import `getSetting`; load custom prompt in `sendMessage`; pass to `getPhaseConfig`
- ✅ **5. `src/main/ipc/handlers.ts`** — import `settingsDb` + `getDefaultSystemPromptTemplate`; register `settings:get`, `settings:set`, `settings:delete`, `settings:getDefaultPrompts`
- ✅ **6. `src/main/preload.ts`** — add `getSettings`, `setSetting`, `deleteSetting`, `getDefaultSystemPrompts` to interface + api object
- ✅ **7. `renderer/src/styles/globals.css`** — append all new CSS rules
- ✅ **8. `renderer/src/components/settings/SystemPromptsSettings.tsx`** — create file (new directory)
- ✅ **9. `renderer/src/components/SettingsPage.tsx`** — create file
- ✅ **10. `renderer/src/components/Header.tsx`** — add `onOpenSettings` prop + ⚙ button
- ✅ **11. `renderer/src/App.tsx`** — add `showSettings` state; import + render `<SettingsPage>`; pass `onOpenSettings` to Header
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- Store session artifacts in ~/.claude-flow/projects/{projectId}/sessions/{sessionId}/
- Artifacts no longer live in project directory - can't be accidentally committed
- Remove .claude-flow/ from .gitignore (not needed anymore)
- Update all IPC handlers and renderer to use projectId instead of projectPath
- Update prompts to remove worktree references
- Update README with new storage location
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- Research phase: reference .claude-flow/sessions/{sessionId}/research.md
- Plan phase: reference .claude-flow/sessions/{sessionId}/plan.md
- Implementation phase: explain worktree isolation and review process
- All phases: mention CLAUDE.md at project root for shared context
- All phases: mention git worktree location .claude-flow/worktrees/{sessionId}/
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- Store artifacts in .claude-flow/sessions/{sessionId}/
- Each session now has isolated research.md and plan.md
- Concurrent sessions no longer conflict
- Add CLAUDE.md support for shared codebase documentation
- Add git worktree creation on session start
- Add git commit/status IPC handlers
- Update all artifact APIs to be session-specific
- Remove artifact clearing on new session (no longer needed)
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- Fix systemPrompt option (was incorrectly using extraArgs)
- Rewrite research phase prompt:
- Emphasize writing to research.md as PRIMARY output
- Explicitly forbid asking about phase transitions
- Add document format template
- Clarify that chat is for questions only
- Rewrite plan phase prompt:
- Same emphasis on plan.md as primary output
- Include code snippet format examples
- Forbid implementation attempts
- Change research/plan permissionMode to acceptEdits (was 'plan')
- 'plan' mode may have been blocking file writes
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- Add @anthropic-ai/claude-agent-sdk dependency
- Implement src/main/claude/phases.ts with phase configs (research/plan/implement)
- Implement src/main/claude/index.ts with SDK wrapper
- query() integration with session management
- Session resume support
- Artifact read/write utilities
- Phase advancement logic
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