refactor: address technical debt with modularization and type safety

[laynepenney]

Summary

Address technical debt in the Codi codebase with four improvements:

1. CLI Module Extraction (~400 lines from index.ts)

• src/cli/history.ts - Command history management
• src/cli/pipeline-input.ts - File/glob resolution with security validation
• src/cli/non-interactive.ts - Single-prompt mode execution
• src/cli/index.ts - Module re-exports

2. Workflow Type Safety

• Add BaseWorkflowStep interface and WorkflowStep discriminated union
• Add 9 type guards (isShellStep, isSwitchModelStep, isLoopStep, etc.)
• Replace as any casts with proper type narrowing

3. Symbol Index Type Safety

• Add hasExtendsMetadata type guard
• Add SymbolMetadataWithExtends interface

4. E2E Test Stability

• Add waitForOutputFlush() helper to ProcessHarness
• Use generic patterns and clearOutput() for robustness

5. Plugin System Investigation

• Create comprehensive docs/PLUGIN-INVESTIGATION.md
• Security analysis and recommendations
• API stability assessment
• Phased re-enablement roadmap

6. Cleanup

• Remove 62 generated workflow files

Metrics

• Reduces as any usage from 30+ to 10 instances
• Extracts ~400 lines from index.ts into focused modules

Test plan

• pnpm build passes with 0 errors
• pnpm test passes (2129 tests)
• Verified workflow type guards work correctly
• E2E tests stable (previously flaky /compact test now robust)

🤖 Generated with Claude Code

[laynepenney]

Self-Review

Verified

• ✅ CI passes (Type Check, Ubuntu tests, macOS tests)
• ✅ +1043/-1553 lines (mostly workflow cleanup deletions)
• ✅ 78 files changed

Changes Reviewed

1. CLI Modules - Properly extracted with security validation in pipeline-input.ts
2. Workflow Type Safety - Discriminated union and type guards correctly implemented
3. Symbol Index Types - hasExtendsMetadata type guard is correct
4. E2E Test Fix - waitForOutputFlush and generic patterns for robustness
5. Plugin Investigation - Comprehensive security analysis and roadmap
6. Workflow Cleanup - 62 generated files removed

No issues found. Ready to merge.