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Comprehensive feature plan covering:
- Three logging levels (default, verbose, debug)
- Wire format capture via --wire-log flag
- Unified callback system across fill/research/run commands

...ements
- Add library-first callback design with structured tool info
- Define enhanced console progress display with search queries/results
- Add emoji indicators and timing information
- Update implementation phases and open questions

...e summaries
- Default mode shows tool calls with queries, timing, result counts, and sources
- Verbose adds top result titles, token counts, tool summary
- Updated FillCallbacks with sources and topResults fields
- Updated examples to reflect new logging levels

Design decisions finalized:
- Wire log format: unify with golden test transcript format
- Debug truncation: 500 chars, configurable in settings.ts
- LOG_LEVEL env var: equivalent to --debug flag
- Web search parsing: show first 5-8 result titles/domains
- Emoji usage: limited set per CLI best practices (✓ ❌ → [tool])
- Callback versioning: clean break, no backward compat
- Non-TTY progress: log lines instead of spinner

...onal details
Default mode now includes:
- Model and provider info at start
- Token counts per turn
- First 5-8 result titles from web search
- Tool summary at end of turn
- Patch validation warnings/errors
Verbose mode now focuses on operational details:
- Harness configuration
- Full web search result listings
- Patch accept/reject with reasons
- Validator execution details
- Form progress stats

Extend the plan spec with support for capturing AI SDK reasoning fields:
- Add WireResponseStep.reasoning field for step-level reasoning
- Add reasoningTokens to usage tracking
- Add onReasoningGenerated callback for library users
- Display reasoning in verbose/debug modes
- New Phase 5 for reasoning capture implementation
Also adds tsx as root dev dependency for running TypeScript scripts.
Based on AI SDK documentation research:
- reasoningText: final step reasoning
- steps[].reasoning: per-step reasoning array
- usage.reasoningTokens: token count for reasoning
- providerMetadata: provider-specific data

Updates to the CLI logging plan:
1. Clarify TTY detection uses existing infrastructure:
 - createSpinnerIfTty() already handles non-TTY
 - shouldUseColors() respects NO_COLOR and TTY
 - picocolors auto-detects - no new implementation needed
2. Add wire format content selection decision (#9):
 - Capture: toolCalls, toolResults, text, reasoning, usage, response.id/modelId
 - Skip: providerMetadata, response.messages (redundant), finishReason per step
 - Keeps wire logs focused and diffable
Based on AI SDK documentation research. Live API testing was blocked by
quota limits on both OpenAI and Anthropic accounts.

Complete Stage 5 validation section with:
Automated Test Coverage:
- Unit tests for logging utils, web search parsing, fill logging
- Callback interface tests for structured tool info
- Wire format tests for AI SDK response capture
- Integration tests for CLI output at each log level
- Cross-command consistency tests (fill, research, run)
- Golden tests for wire format and log level outputs
Manual Validation Checklist:
- Visual console output review at each log level
- TTY vs non-TTY behavior (colors, spinner, NO_COLOR)
- Wire log YAML review for completeness and diffability
- Environment variable behavior (LOG_LEVEL, MARKFORM_WIRE_LOG)
- Error handling scenarios
- Library API validation with TypeScript callbacks
- Cross-command visual comparison
- Documentation accuracy verification
Acceptance and Regression Checks:
- All 7 acceptance criteria from Stage 1
- 5 regression checks for existing behavior

Expands validation plan Stage 5 with senior-engineer-level test coverage:
- Edge cases: empty forms, large forms, Unicode, truncation boundaries
- Error paths: network failures, auth errors, file system errors, interrupts
- Security: API key redaction, PII handling, file permissions
- Performance: memory usage, I/O benchmarks, scalability targets
- Compatibility matrix: Node versions, OS, terminals, CI environments
- Graceful degradation: partial failures, missing features, backward compat

This PR implements the CLI logging improvements outlined in the plan spec:
- Added `LogLevel` type: quiet, default, verbose, debug
- Added `--debug` CLI flag for full diagnostic output
- Added `logDebug()` function for debug-level messages
- Added `MARKFORM_LOG_LEVEL` environment variable support
- Added `--wire-log <path>` flag to fill and research commands
- Added `MARKFORM_WIRE_LOG` environment variable support
- Captures full LLM request/response in YAML format
- Extended `FillCallbacks` with `toolType`, `query`, `resultCount`, `sources`, `topResults`
- Added `toolParsing.ts` with web search result extraction
- Shows search queries in yellow, results summary in default output
- Full result listings available in verbose mode
- Updated `fillLogging.ts` to respect all log levels
- Updated research command to use `createFillLoggingCallbacks`
- Consistent output format across fill and research commands
- New: `src/harness/toolParsing.ts`
- New: `docs/project/specs/active/valid-2026年01月04日-agent-cli-logging-improvements.md`
- Modified: CLI, harness, and test files
- All 1432 unit tests pass
- TypeScript strict mode passes
- ESLint with --max-warnings 0 passes
- Build succeeds

- Add WireReasoningContent type and reasoning field to WireResponseStep
- Add reasoningTokens to WireResponseFormat usage
- Extract reasoning from AI SDK responses in liveAgent
- Call onReasoningGenerated callback when reasoning present
- Include reasoning in wire format YAML output
- Trim plan spec validation section from 1158 to 764 lines
- Move detailed test checklists to validation spec reference
- Close markform-545 and markform-546 beads

- Add --wire-log flag to run command for consistency with fill/research
- Add transcript field to FillResult type for wire format capture
- Update programmaticFill to build transcript when captureWireFormat is enabled
- Add Log Levels and Wire Format Capture sections to development.md
- Update validation spec with run command testing and complete file list

- Add --trace flag for incremental file logging during execution
- Add MARKFORM_TRACE env var support for trace file
- Increase DEBUG_OUTPUT_TRUNCATION_LIMIT from 500 to 2000 chars
- Make truncation limit configurable via MARKFORM_DEBUG_TRUNCATION_LIMIT
- Fix run.ts to pass model info to createFillLoggingCallbacks
- Add traceFile support to research.ts callbacks
- Document logging system review findings
Trace file support allows monitoring long-running fills by writing
log output incrementally to a file (without ANSI colors), useful for
debugging and post-hoc analysis.

- Add trace file support to fill.ts command (addresses Codex review)
- Update tryscript tests to include new --debug and --trace options
- Update README test to use more flexible badge matching
The --trace flag was previously only working in run/research commands.
This fix adds the same incremental file logging support to the fill command.

- Add comprehensive manual validation steps for trace file feature
- Update test counts (1455 unit tests, 18 tryscript tests)
- Add edge cases and error handling verification steps
- Document combined flags testing scenarios
- Add potential issues to watch for section

...traceUtils
Per PR review feedback:
- Remove --wire-log flag from fill, research, and run commands
- Use only global --trace flag for all trace file output
- Create shared traceUtils.ts library with common utilities:
 - stripAnsi: Remove ANSI codes from strings for file output
 - createTracer: Create trace function for file logging
 - truncate: Truncate strings with ellipsis for debug output
 - formatDuration: Format milliseconds as human-readable
 - formatBytes: Format file sizes as human-readable
- Update fillLogging.ts to use shared utilities
- Remove duplicate code and unused imports
This reduces code duplication and provides a cleaner API where
trace output is controlled via the global --trace flag.

Add trace file output to the run command for consistency with
fill and research commands. Now all form-filling commands log
workflow configuration, completion status, and timing to the
trace file when --trace is specified.

Create reusable formatUtils.ts with general-purpose formatting utilities:
- stripAnsi: Remove ANSI escape codes from strings
- safeTruncate: Truncate strings with ellipsis (renamed from truncate)
- formatDuration: Format milliseconds as human-readable
- humanReadableSize: Format bytes as human-readable (renamed from formatBytes)
traceUtils.ts now imports from formatUtils.ts and re-exports for
backward compatibility. This allows these utilities to be reused
across the codebase, not just in CLI trace code.

Scripts use 'npx tsx' which works without a local dependency.
This was added unnecessarily in a previous commit.

- Support both 'text' and 'content' property names for reasoning items
 since different AI providers may use different property names
- Add fallback message when reasoning content is not available
- Add tests for reasoning callback in fillLogging

Add end-to-end tests for CLI logging at different verbosity levels:
- Default mode: shows turn and patch info
- Verbose mode: shows config details (max turns, patches, roles)
- Quiet mode: suppresses turn output
- Trace file: verifies file creation, header format, content
- Output verification: file creation and content checks
- User role fill with --roles flag
These tests run actual fill commands with mock agents and verify
the logging output matches expected patterns.

- Add test results table showing pass/fail status for all logging features
- Mark --quiet flag bug (markform-8): session transcript still printed
- Document completed manual testing for default, verbose, debug, trace modes
- Note live agent testing blocked by network issues
- Add bead markform-8 for quiet mode bug tracking

Address PR review comments:
- Fix fill command --trace flag which was silently ignored (2660027464)
- Add trace file output to createCliToolCallbacks for tool/LLM/reasoning logs
- Move safeStringify() to shared formatUtils.ts library (2660068669)
- Re-export safeStringify from traceUtils.ts for convenience
All 11 PR #84 review comments are now fully addressed.

Update validation plan with detailed test results from systematic testing:
- Mock mode at all log levels (default, quiet, verbose, debug)
- Trace file output with ANSI stripping verification
- Session recording (--record flag)
- Document known bug markform-8 (quiet mode doesn't suppress transcript)
- Add reviewer testing checklist for live agent tests
- Remove outdated --wire-log references (flag removed)
- Document all 11 PR review comments addressed

- Live agent testing now passing with GPT-4.1-mini
- Token counts, LLM call logging, tool tracking all verified
- Trace file captures all LLM/tool activity
- Required undici ProxyAgent for containerized environment
- All core logging features confirmed working

OpenAI's web_search tool executes server-side (no local execute function),
so the callback wrapping was skipping it. This fix:
1. Modified wrapToolsWithCallbacks to return both wrapped tools and set of
 wrapped tool names for tracking
2. Added code in step processing loop to fire onToolStart/onToolEnd
 callbacks for non-wrapped tools using step results
3. Fixed AI SDK type property names: input not args, output not result
This ensures [web_search] "query" and tool results are logged to console
during live agent execution.