…me MCP tools

Resolved conflicts: kept tools field removed from agent files (from PR buildermethods#294)
while incorporating the Chrome tool expansion function in common-functions.sh

…pstream PR buildermethods#294

Adapt improvements from buildermethods/agent-os PR buildermethods#294 to work with our
JSON-based workflow system. These changes prevent false task completion and
improve refactoring task handling.

Changes to implement-tasks.md:
- Add CLAUDE.md reading instruction for project-specific rules
- Add skills discovery via <available_skills> section
- Add 6 critical task completion rules:
  - Rule 1: Tasks complete only when actually executed
  - Rule 2: Handle missing prerequisites (start services, don't install deps)
  - Rule 3: Task groups require all tasks complete
  - Rule 4: TDD phases require actual test execution
  - Rule 5: Verification tasks require evidence
  - Rule 6: Incomplete tasks must stay incomplete

Changes to create-tasks-list.md:
- Add Step 1.5: Spec completeness verification for refactoring tasks
- Run grep searches to find all affected files before creating tasks
- Document gaps between spec and actual codebase impact

Changes to research-spec.md:
- Add Question 8 for impact analysis during requirements gathering
- Add Impact Analysis section to requirements.md template
- Capture affected areas for refactoring tasks

Changes to write-spec.md:
- Add Step 2.5: Comprehensive impact analysis for refactoring
- Add "Files Requiring Modification" section to spec.md template
- Check for duplicate definitions and related mappings

Note: PRs buildermethods#301 (Chrome alias) and buildermethods#292 (separate subagents) were already
merged. PR buildermethods#293 (init-spec clarity) not applicable due to JSON workflow rewrite.

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