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refactor: reorganize codebase into proper pnpm workspace packages (#45)

* refactor: reorganize codebase into proper pnpm workspace packages

- Create @thumbcode/types package with domain-specific type definitions
  - agents, projects, workspaces, credentials, chat, user, navigation, api, events
- Create @thumbcode/config package with environment and app configuration
  - env.ts with environment validation
  - constants.ts with API URLs, OAuth config, storage keys
  - features.ts with feature flag system
- Update @thumbcode/core with full GitService and CredentialService implementations
  - GitService.diff() now uses tree-walking algorithm for proper diffs
  - CredentialService with expo-secure-store and biometric auth
- Update @thumbcode/state with complete Zustand stores
  - agentStore, chatStore, credentialStore, projectStore, userStore
  - All stores have devtools, persist middleware, and selectors
- Update @thumbcode/ui with modern NativeWind v4 patterns
  - Remove deprecated styled() API usage
  - Add ThemeProvider with P3 "Warm Technical" tokens
  - Proper primitives, form, feedback, and layout components
- Fix linter warnings:
  - Reduce cognitive complexity in GitService.status() with lookup map
  - Fix non-null assertions in test files
- All 114 tests passing

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* fix: replace deprecated substr() with slice()

Replace all instances of .substr(2, 9) with .slice(2, 11) across:
- packages/state/src/*.ts
- src/stores/*.ts
- packages/agent-intelligence/src/components/chat/ChatInput.tsx

The substr() method is deprecated in favor of slice().

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

160 of 483 branches covered (33.13%)

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7 of 10 new or added lines in 5 files covered. (70.0%)

410 of 775 relevant lines covered (52.9%)

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