- Add configurable quality_gate settings to config.yml (agent_review_command,
  default_timeout, default_max_attempts)
- Update installer to create quality_gate config section with defaults
- Refactor QualityGate to separate system instructions from user payload
- Use -s flag to pass instructions as system prompt to review agent
- Change file separator format to 20 dashes for clearer delineation
- Remove step_instructions from QualityGate interface (not useful for review)
- Add quality_review_override_reason to finished_step to skip quality gate
- Add JSON schema validation for quality gate responses
- Add comprehensive integration tests with mock review agent subprocess
- Remove block_bash_with_instructions hook (commit skill not available)

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

- Update e2e tests for Claude Code integration
- Add quality_criteria to fruits job fixture
- Fix test assertions for updated install flow
- Minor sync.py adjustments

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

The rules system was removed in commit 6b3e1a2. This cleans up
stale documentation references to rules_check in hook-related code.

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

- StateManager now uses a session stack instead of single active session
- Starting a workflow while one is active pushes onto the stack
- Completing a workflow pops from stack and resumes parent
- Added abort_workflow tool with explanation parameter
- All tool responses include stack field [{workflow, step}, ...]
- Added logging to all MCP tool calls with stack info
- Updated server instructions to document nesting and abort

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

- Add `from None` to raise in except clause (B904)
- Remove unused variables in tests (F841)
- Rename unused loop variable to underscore prefix (B007)
- Apply ruff formatting to 14 files

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

Replace flake-utils with uv2nix/pyproject-nix for proper Python
dependency management in Nix. This provides hermetic builds directly
from uv.lock and supports editable installs for development.

Key changes:
- Use uv2nix to generate Python package set from uv.lock
- Add pyproject-build-systems for build dependency resolution
- Add editables to build-system requires (needed by hatchling for
  editable wheel builds)
- Remove .venv management from shell hook (Nix handles it now)

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

- Fix quality_gate.py to handle Claude CLI --output-format json wrapper
  objects by extracting the 'result' field before parsing
- Add tests for wrapper object handling with strong comments explaining
  the mock design
- Remove deprecated 'exposed' field from learn step in deepwork_jobs
- Add 'learn' workflow to make orphaned step accessible via MCP
- Add 'update' workflow to update job for MCP compatibility
- Migrate stop_hooks to quality_criteria in update job
- Clean up settings.json by removing obsolete Skill permissions

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

Document the major architectural changes including:
- New MCP server with checkpoint-based workflow execution
- Removal of the rules system
- Simplified skill generation
- New deepwork_jobs steps

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

Mark 0.7.0 as alpha prerelease so that `uv add deepwork` continues
to install the stable 0.5.1 by default, requiring explicit version
specification for the new alpha.

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