trinity-method-sdk 2.0.9 → 2.2.0

package/CHANGELOG.md

@@ -1,267 +1,702 @@
-# Changelog
-
-All notable changes to Trinity Method SDK will be documented in this file.
-
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-
-## [Unreleased]
-
-### Added
-
-### Changed
-
-### Deprecated
-
-### Removed
-
-### Fixed
-
-### Security
-
-## [2.0.9] - 2026-01-12
-
-### Changed
-
-- **Trinity-docs command specification** - Added evidence-based documentation verification
-  - Added Rule 2: Evidence-Based Documentation Only - prevents documenting uninstalled tools
-  - Added Phase 1 Step 6: Tool & Feature Verification for all project types
-  - Added tool verification report to Phase 5 output
-  - Prevents aspirational/best-practice content that doesn't exist in codebase
-  - Addresses incident where Lighthouse was documented without being installed
-
-- **Trinity-readme command specification** - Removed Trinity self-documentation conflicts
-  - Deleted Type C Template that documented Trinity infrastructure (violated Rule 1)
-  - Added Rule 1 Enforcement Checklist with verification commands
-  - Added Phase 1 Step 4.5: Filter Gitignored and Trinity Directories
-  - Added Trinity Detection Warning to explicitly skip trinity/ and .claude/
-  - Removed trinity/ from glob patterns and project structure examples
-  - Addresses incident where trinity/ was included in README file tree despite being gitignored
-
-- **Trinity-readme command specification** - Added LICENSE file verification for badges
-  - Added Phase 1 Step 7: License Verification - reads actual LICENSE file
-  - LICENSE file is now source of truth (priority over package.json)
-  - Detects license type from file header (MIT, ISC, Apache, GPL, BSD, etc.)
-  - Warns when package.json license field doesn't match LICENSE file
-  - Falls back to package.json only if LICENSE file doesn't exist
-  - Addresses incident where ISC badge was generated despite MIT LICENSE file
-
-- **Trinity-docs command specification** - Added Trinity reference sanitization enforcement
-  - Added Rule 1 Forbidden Patterns - explicit list of patterns that must not appear in docs/
-  - Added Phase 4.5: Trinity Reference Sanitization - scans and removes Trinity references
-  - Added Rule 1 Compliance verification to Phase 5 report with pass/fail status
-  - Removed Trinity report link from docs/README.md template footer
-  - Prevents Trinity Method, agent names, commands, and infrastructure references in user docs
-  - Addresses incident where 7 documentation files contained Trinity Method references
-
-## [2.0.8] - 2026-01-08
-
-### Added
-
-- **Bot directory support** - Added `bot/` as a recognized source directory
-  - `bot/` directory now detected during deployment
-  - Framework-specific CLAUDE.md automatically deployed to `bot/` directory
-  - Supports nested patterns: `bot/src`, `bot/lib`, `bot/app`, `src/bot`
-
-- **Force update flag** - Added `--force` flag to `trinity update` command
-  - Allows forcing re-update even when already at latest version
-  - Useful for repairing corrupted deployments or applying template fixes
-  - Usage: `trinity update --force`
-
-## [2.0.7] - 2026-01-06
-
-### Fixed
-
-- **CRITICAL: Agent file extension handling** - Fixed agent updates to strip `.template` extension
-  - Agents were being copied with `.md.template` extension, creating duplicates alongside old `.md` files
-  - Now correctly strips `.template` extension during deployment to `.claude/agents/` subdirectories
-  - Each agent file copied individually with proper extension handling
-
-- **CRITICAL: Template directory structure** - Fixed template updates to use correct directory structure
-  - Work order templates were being deployed to wrong directory (`trinity/templates/` instead of `trinity/templates/work-orders/`)
-  - Documentation templates (`trinity/templates/documentation/`) were not being updated at all
-  - Investigation templates (`trinity/templates/investigations/`) were not being updated at all
-  - Now correctly deploys all 3 template types to their proper subdirectories with `.template` extension stripped
-  - Total templates updated: 13 files (6 work-orders + 2 documentation + 5 investigations)
-
-## [2.0.6] - 2026-01-06
-
-### Fixed
-
-- **CRITICAL: Command categorization logic** - Fixed `trinity update` to correctly categorize slash commands
-  - Execution commands (`audit`, `changelog`, `docs`, `readme`) were falling through to utility category
-  - Investigation commands containing `investigate` were not being matched properly
-  - Commands now deploy to correct category directories (session, planning, execution, investigation, infrastructure, infrastructure, utility)
-  - Prevents duplicate commands in wrong directories during updates
-
-## [2.0.5] - 2026-01-06
-
-### Fixed
-
-- **CRITICAL: Slash command file updates** - Fixed `trinity update` command file extension handling
-  - Update commands module was looking for `.md` files but templates use `.md.template` extension
-  - Now correctly processes `.md.template` files and strips extension for deployed files
-  - Slash commands now update properly (20 command files) when running `trinity update`
-  - Matches the pattern used by knowledge-base update module
-
-## [2.0.4] - 2026-01-06
-
-### Fixed
-
-- **CRITICAL: Update command path resolution** - Fixed `trinity update` to use centralized SDK path resolution
-  - Update command was using hardcoded `@trinity-method/sdk` path instead of `trinity-method-sdk`
-  - Commands, agents, templates, and knowledge base files now update correctly with global installations
-  - Fixed "Commands template path not found, skipping" warning
-
-## [2.0.3] - 2026-01-06
-
-### Fixed
-
-- **CRITICAL: Global install support** - Fixed SDK path resolution to work with global installations
-  - Changed package name from incorrect `@trinity-method/sdk` to `trinity-method-sdk` in path resolution
-  - Added `import.meta.url` support for resolving SDK location in global installs
-  - `trinity update` command now works correctly when SDK is installed globally
-  - Fixed "ENOENT: no such file or directory" error when running update command
-
-## [2.0.2] - 2026-01-02
-
-### Added
-
-- **DOCUMENTATION RULES** section to all APO documentation commands (`/trinity-docs`, `/trinity-readme`, `/trinity-changelog`)
-  - Rule 1: No Self-Serving Trinity Documentation - Prevents APO from including Trinity Method information in user project documentation
-  - Provides clear ✅/❌ examples and rationale for focusing exclusively on user's codebase
-- Explicit **Write tool execution commands** throughout `/trinity-docs` Phase 2
-  - Added 🚨 CRITICAL EXECUTION REQUIREMENT section at Phase 2 start
-  - Added **EXECUTION REQUIRED** code blocks for each seeding step
-  - Added **Phase 2 Execution Summary** with mandatory file creation checklist
-  - Ensures APO creates actual documentation files instead of just showing templates
-
-### Changed
-
-- **`/trinity-docs` command:** Enhanced Phase 2 with explicit Write tool requirements
-  - Step 2 (Guides): Added execution requirements for getting-started.md and framework-specific guides
-  - Step 3 (API): Added execution requirements for api/README.md
-  - Step 4 (Architecture): Added execution requirements for architecture/overview.md
-  - Step 5 (Reference): Added execution requirements for reference/README.md
-  - Phase now requires minimum 4 files to be created: getting-started.md, api/README.md, architecture/overview.md, reference/README.md
-
-### Fixed
-
-- **APO file creation issue:** `/trinity-docs` now explicitly commands APO to use Write tool, preventing scenario where directory structure is created but documentation files are not written
-
-## [2.0.1] - 2025-12-29
-
-### Added
-
-- Installation instructions in README.md with npx and global install options
-- Automatic npm deployment on every push to main branch via GitHub Actions CD workflow
-
-### Changed
-
-- **CD Workflow:** Modified to deploy to npm on all main branch pushes (not just version tags)
-- **CD Workflow:** GitHub releases now only created for version tags, not regular commits
-- Updated all package references from `@trinity-method/cli` to `trinity-method-sdk`
-
-### Fixed
-
-- Removed redundant `node_modules/` from Trinity's .gitignore additions
-
-## [2.0.0] - 2025-12-21
-
-### Added
-
-- **Agent System Expansion:** Grew from 7 to 19 specialized agents
-  - **Planning Layer (4 agents):** MON (Requirements Analyst), ROR (Design Architect), TRA (Work Planner), EUS (Task Decomposer)
-  - **Execution Layer (3 agents):** KIL (Task Executor), BAS (Quality Gate), DRA (Code Reviewer)
-  - **Support Layer (4 agents):** APO (Documentation Specialist), BON (Dependency Manager), CAP (Configuration Specialist), URO (Refactoring Specialist)
-  - **Leadership & Audit (2 agents):** ALY (Chief Technology Officer), JUNO (Quality Auditor)
-  - **Infrastructure (5 agents):** TAN, ZEN, INO, EIN, AJ MAESTRO (legacy)
-- Increased deployment from 49 to 64 production-ready components
-- Expanded slash commands from 8 to 20 commands across 6 categories
-  - Session Management: `/trinity-start`, `/trinity-continue`, `/trinity-end`
-  - Planning: `/trinity-requirements`, `/trinity-design`, `/trinity-decompose`, `/trinity-plan`
-  - Execution: `/trinity-orchestrate`, `/trinity-audit`, `/trinity-readme`, `/trinity-docs`, `/trinity-changelog`
-  - Investigation: `/trinity-create-investigation`, `/trinity-plan-investigation`, `/trinity-investigate-templates`
-  - Infrastructure: `/trinity-init`
-  - Utility: `/trinity-verify`, `/trinity-agents`, `/trinity-workorder`
-- Enhanced `/trinity-readme` command template to v2.0.0 with comprehensive validation phases
-  - Phase 2h: Command/Script/CLI Validation - Verifies all documented commands exist in codebase
-  - Phase 2i: Code Example Validation - Checks code examples match current API signatures
-  - Phase 2j: API/Function Reference Validation - Verifies documented functions/classes exist
-  - Phase 2k: Dependency Claims Validation - Cross-references README with package manifests
-  - Phase 2l: Stale Content Detection - Finds TODO markers, outdated dates, placeholder text
-
-### Changed
-
-- **BREAKING:** Updated Trinity Method to v2.0.0 architecture
-- **Agent System:** Complete agent architecture redesign with specialized layers
-- **Documentation System:** Enhanced APO capabilities with comprehensive audit phases
-- Refactored 7 functions to reduce cyclomatic complexity (all ≤15)
-- Improved code maintainability and readability across codebase
-- Enhanced test coverage and reliability (405 tests, 100% passing)
-
-### Deprecated
-
-- AJ MAESTRO orchestrator (v1.0) replaced by ALY in v2.0
-
-### Fixed
-
-- Template path resolution in integration tests
-- Linting deployment tests now correctly locate template files
-- **Documentation Accuracy:** Fixed 6 critical inaccuracies in README.md
-  - Removed 24+ non-existent CLI commands (`npx trinity investigate`, `crisis`, `analytics`, etc.)
-  - Fixed 13 broken documentation links (docs/methodology/, docs/adr/, docs/workflows/)
-  - Corrected agent count inconsistencies throughout documentation (unified to 19 agents)
-  - Updated deployment examples to reflect actual CLI (`npx @trinity-method/cli deploy/update`)
-- Fixed broken ADR links in src/README.md (replaced with design principles summary)
-- Fixed broken ADR links in docs/README.md (removed non-existent file references)
-
----
-
-## [1.0.1] - 2025-10-02 (Legacy - @trinity-method/cli)
-
-### Fixed
-
-- **Critical:** Missing template files in npm package (only 9 of 36 were included)
-- Fixed file paths to use bundled templates instead of workspace structure
-- All `.md.template` files now properly included in published package
-- Updated `deploy.js` and `update.js` to reference correct template locations
-- Bundled agents and hooks directly into CLI package for standalone operation
-
-### Changed
-
-- Reorganized package structure to be self-contained when published to npm
-- Templates, agents, and hooks now bundled in `packages/cli/templates/`
-
-**Note:** This version was published as `@trinity-method/cli`. Starting with v2.0.0, the package was renamed to `trinity-method-sdk`.
-
----
-
-## [1.0.0] - 2025-10-01 (Legacy - @trinity-method/cli)
-
-### Added
-
-- Initial release of Trinity Method SDK for Claude Code
-- 7 specialized Trinity agents (Aly, AJ, TAN, ZEN, INO, Ein, JUNO)
-- Claude Code-exclusive deployment
-- Interactive deployment with linting and CI/CD configuration
-- Linting configuration (ESLint, Prettier, etc.)
-- CI/CD automation (GitHub Actions, GitLab CI)
-- Matrix testing support
-- Coverage integration (Codecov, Coveralls)
-- Employee Directory with agent documentation
-- Trinity structure (knowledge-base, templates)
-- CLAUDE.md context file deployment
-- README injection for Trinity Method section
-- 8 slash commands (/trinity-init, /trinity-verify, /trinity-docs, /trinity-start, /trinity-continue, /trinity-end, /trinity-workorder, /trinity-agents)
-- Session management with archival system
-- Comprehensive CLI documentation
-
-### Strategic Decision
-
-- Focused exclusively on Claude Code for exceptional user experience
-- Community contributions welcome for other coding agents
-
-**Note:** This version was published as `@trinity-method/cli`. Starting with v2.0.0, the package was renamed to `trinity-method-sdk`.
-
-[1.0.0]: https://github.com/lukadfagundes/trinity-method-sdk/releases/tag/v1.0.0
+# Changelog
+
+All notable changes to Trinity Method SDK will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [2.2.0] - 2026-02-24
+
+### Added
+
+- **Markdown linting in CI pipeline and pre-commit hook** - Added blocking `markdownlint-cli2`
+  validation for `*.md`, `docs/**/*.md`, and `src/**/*.md` in both CI and pre-commit
+  - CI: Added lint step to `docs` job in `.github/workflows/ci.yml`
+  - Pre-commit: Added Stage 4 to `.husky/pre-commit` running markdownlint on all tracked
+    markdown directories
+  - Enforces markdown syntax standards across all 78 markdown files using
+    `.markdownlint.json` config
+- **New `/trinity-breakdown` slash command** - Guided, user-driven implementations where CC
+  acts as an instructor walking users through changes step-by-step instead of executing them
+  directly (Issue #11)
+- **GitHub Releases workflow** - Automated draft release creation on version tags (`v*.*.*`)
+  via `.github/workflows/release.yml` (Issue #5)
+  - 5-job pipeline: version extraction, CHANGELOG release notes extraction,
+    tag-vs-package.json version validation, full CI quality gates, and draft GitHub release
+  - Uses `softprops/action-gh-release@v2` with `draft: true` — releases require manual
+    publishing
+  - CHANGELOG extraction uses Node.js script (not sed) matching `## [X.Y.Z]` Keep a
+    Changelog format
+  - Fails fast on version mismatch or missing/empty CHANGELOG section
+  - Coverage thresholds mirror CI pipeline: lines >= 75%, branches >= 65%,
+    functions >= 80%, statements >= 75%
+  - No `npm publish` automation — publishing remains manual via `npm publish`
+
+### Changed
+
+- **Enabled all TypeScript strict mode flags** - Turned on `strictNullChecks`,
+  `strictPropertyInitialization`, `noUnusedLocals`, and `noUnusedParameters` in
+  tsconfig.json (Issue #6)
+  - All four flags were previously disabled, weakening compile-time type safety
+  - Codebase required zero changes for `strictNullChecks` and
+    `strictPropertyInitialization` (already null-safe)
+  - Prefixed 6 unused parameters with `_` to satisfy `noUnusedParameters`
+    (5 in `deploy-linting.ts`, 1 in `summary.ts`)
+  - All 417 tests pass, 0 type errors, lint clean
+- **Added metrics module test coverage** - Created comprehensive test suites for
+  `dependency-parser.ts` and `framework-detector.ts` (Issue #6)
+  - `dependency-parser.ts` coverage: 9.37% → 100% (23 tests covering Node.js, Python,
+    Rust, Flutter, Go, and error paths)
+  - `framework-detector.ts` coverage: 36.36% → 95.23% (24 tests covering all version
+    detectors and package manager detection)
+  - Overall project coverage improved from 83% → 89% (464 tests total)
+- **Fixed all 32 devDependency vulnerabilities** - Resolved minimatch ReDoS, ajv ReDoS,
+  and markdown-it ReDoS via `npm audit fix` and `overrides` in package.json (Issue #6)
+  - `npm audit fix` resolved ajv (<6.14.0), markdown-it (13.0.0-14.1.0), and
+    @isaacs/brace-expansion (5.0.0) — 9 vulnerabilities
+  - Added `overrides` for `minimatch@^10.2.1` to force resolution of 23 remaining
+    transitive dependency vulnerabilities through eslint, jest, and typedoc
+  - `npm audit` now reports 0 vulnerabilities (was 32: 30 high, 2 moderate)
+- **Restructured `trinity/` into `.claude/trinity/`** - Consolidated deployment footprint
+  from two top-level directories to one (Issue #3)
+  - `trinity deploy` now creates `.claude/trinity/` instead of a separate `trinity/`
+    directory
+  - `trinity update` manages `.claude/trinity/` with consolidated backup (single `.claude/`
+    backup covers everything)
+  - All 50+ template files updated with new deployment target paths
+  - All relative paths recalculated for new directory depth
+  - 417 tests pass with restructured paths
+- **Updated `.gitignore` entries** - Trinity deployment now only ignores
+  `.claude/trinity/archive/` and `.claude/trinity/templates/` instead of all `.claude/`,
+  `*CLAUDE.md`, `TRINITY.md`, and `trinity/` allowing agents, commands, and context files
+  to be tracked in version control
+- **Removed `.claude/trinity/patterns/` directory** - No longer deployed as an empty
+  placeholder; directory structure reduced from 17 to 16 directories
+
+### Fixed
+
+- **Resolved ~600 markdownlint violations across 78 markdown files** - Fixed all markdown
+  syntax errors in `docs/`, root (`*.md`), and `src/` directories (Issue #6)
+  - `docs/` (72 files): ~580 violations fixed (MD013 line length, MD022 blanks around
+    headings, MD031/MD032 blanks around fences/lists, MD040 code fence languages, MD009
+    trailing spaces, MD036 emphasis as heading, MD026 trailing punctuation)
+  - `README.md`: 16 violations fixed (MD013, MD022, MD026, MD036, MD040)
+  - `CONTRIBUTING.md`: 6 violations fixed (MD013, MD009, MD031, MD032, MD040)
+  - `CLAUDE.md`: 4 violations fixed (MD022 blanks around headings)
+  - `src/CLAUDE.md`: 42 violations fixed (MD022, MD031, MD032, MD040, MD013)
+  - `src/README.md`: 3 violations fixed (MD013, MD040)
+  - Updated `.markdownlint.json` config: added `siblings_only: true` to MD024 for Keep a
+    Changelog duplicate heading compatibility
+
+- **CRITICAL: Pre-commit hooks non-functional for Node.js** - Switched from Python's
+  pre-commit framework to husky + lint-staged for Node.js/React projects (Issue #4)
+  - Node.js/React projects now deploy `.husky/pre-commit` with `npx lint-staged` instead
+    of `.pre-commit-config.yaml`
+  - Added `husky@^9.1.7` and `lint-staged@^16.2.0` as devDependencies with
+    `prepare: 'husky'` script
+  - Hooks activate automatically on `npm install` — no manual setup required
+  - `lint-staged` configuration injected into `package.json` (eslint + prettier for TS/JS,
+    prettier for JSON/MD/YAML)
+  - Python/Flutter/Rust projects continue to use `.pre-commit-config.yaml` (unchanged)
+  - Existing pre-commit configurations detected and preserved (`.husky/`,
+    `.pre-commit-config.yaml`, or husky/lint-staged in package.json)
+
+- **CRITICAL: CI/CD workflow templates never deployed** - Fixed `enableCICD` from
+  interactive config never bridging to `ciDeploy` deployment flag
+  - Added bridge in deploy orchestrator:
+    `if (config.enableCICD) { options.ciDeploy = true; }`
+  - CI templates now correctly deploy when user selects CI/CD during `trinity deploy`
+
+- **CI template variables not processed** - Added `processTemplate()` call to CI workflow
+  deployment
+  - `{{PROJECT_NAME}}`, `{{FRAMEWORK}}`, and other template variables now resolve in
+    deployed `ci.yml`
+  - Passes variables from deploy orchestrator through `deployCICD()` to
+    `deployCITemplates()`
+
+- **No --force protection for GitHub Actions templates** - Added existence check matching
+  GitLab's pattern
+  - `.github/workflows/ci.yml` now skipped if it already exists (unless `--force` is used)
+  - Both GitHub and GitLab platforms now have consistent `--force` flag protection
+
+- **Configuration display showed wrong filename** - Changed `trinity-ci.yml` to `ci.yml`
+  in interactive prompt output
+  - Both detected-platform and unknown-platform display now show correct filename
+
+- **CI workflow template header** - Changed `CI/CD Pipeline` to `CI Pipeline` in
+  `ci.yml.template`
+
+### Removed
+
+- **`TRINITY.md` root file** - No longer deployed; Trinity context is now at
+  `.claude/trinity/CLAUDE.md`
+  - Deleted `src/templates/root/TRINITY.md.template`
+  - Removed `deployTrinityMarkdown()` function from deploy pipeline
+- **Dead template files** - Deleted `cd.yml.template` (used undefined `{{DOMAIN}}`
+  variable) and `github-actions.yml` (orphaned, never referenced)
+- **CD workflow references** - Removed all Continuous Deployment workflow references from
+  source code, templates (EIN, TAN, init, verify), CI workflow, tests, and documentation
+
+## [2.1.0] - 2026-01-21
+
+### Added
+
+- **NEW: Trinity-docs-update command** - Comprehensive documentation update system for
+  maintaining existing docs
+  - **Command:** `/maintenance:trinity-docs-update` - Updates existing documentation to
+    reflect codebase changes
+  - **Architecture:** JUNO audit → 3 parallel APO instances → JUNO verification loop →
+    Final quality audit
+  - **Autonomous Execution:** Runs from start to finish without user intervention unless
+    errors occur
+  - **Version:** 2.0.9
+  - **Last Updated:** 2026-01-19
+
+- **Trinity-docs-update - JUNO audit system** - Phase 1 comprehensive codebase analysis
+  with mandatory verification protocols
+  - **Database Verification Protocol (Mandatory):**
+    - Step 1: Detect database presence via bash detection script
+    - Step 2: **MANDATORY** production database connection attempt if database detected
+    - Documents connection info search (.env, docker-compose.yml, config files)
+    - Documents connection attempt method and result (success/failure with reason)
+    - Falls back to schema files ONLY after documented connection failure
+    - Prevents documentation based on outdated schema files
+  - **Environment Configuration Verification Protocol (All Projects):**
+    - Priority 1: Check actual environment files (.env, .env.local) FIRST
+    - Priority 2: Check template files (.env.example)
+    - Priority 3: Check code defaults (|| fallback values)
+    - Documents all findings and discrepancies
+    - Source of truth order: Actual config > Template > Code defaults
+    - **Prevents false positives:** Won't flag correct docs as wrong by verifying against
+      actual config
+  - **Business Logic Discovery:** Scans controllers, services, models, utilities at
+    function-level granularity
+  - **Output:** `trinity/reports/DOCS-UPDATE-AUDIT-{{DATE}}.md` with APO work assignments
+
+- **Trinity-docs-update - Configuration false positive prevention** - Resolution rules
+  prevent incorrect audit findings
+  - **Resolution Rule 1:** If .env sets value X, then X is correct (docs showing X are
+    correct)
+  - **Resolution Rule 2:** Code defaults contradicting .env should be fixed (not docs)
+  - **Resolution Rule 3:** Documentation showing actual config value is NEVER wrong
+  - **Example:** Port 3001 in docs + .env, but code shows `|| 4000` → docs are correct,
+    code default needs fixing
+  - **Impact:** Eliminates false positives where JUNO would flag correct documentation as
+    wrong
+
+- **Trinity-docs-update - Scope boundary with consistency exceptions** - Defines strict
+  boundaries with limited exceptions
+  - **ALLOWED:** Read any file, write/edit files in docs/ directory only
+  - **FORBIDDEN:** Modify source code, database schemas, config files, build files, tests
+  - **EXCEPTIONS (APO-1 only):**
+    - Fix hardcoded default values contradicting documented standards
+      (e.g., `|| 4000` → `|| 3001`)
+    - Update .env.example template values to match actual standards
+    - ONLY simple constant/default changes (no logic modifications)
+    - MUST verify against actual .env first
+  - **Scenario C Example:** Docs show port 3001, .env has 3001, code default is 4000 →
+    Fix code default to 3001
+
+- **Trinity-docs-update - APO parallel execution system** - Phase 2 launches three
+  documentation specialists concurrently
+  - **APO-1:** Base documentation updates (architecture, setup, guides)
+    - **NEW:** Configuration consistency fixes (simple defaults that contradict standards)
+    - Update .env.example to match actual standards
+    - Align configuration values across codebase and docs
+    - Restriction: Only simple constants (no logic changes)
+  - **APO-2:** Update existing business logic documentation OR new docs (first half)
+  - **APO-3:** New business logic documentation (second half)
+  - Each APO creates personal checklist from JUNO's audit report
+  - All APOs verify changes against actual codebase (not assumptions)
+  - Output: Updated/new documentation files in docs/
+
+- **Trinity-docs-update - APO verification requirements** - Mandatory codebase
+  verification for all documentation changes
+  - **For EVERY change, APO must:**
+    1. Identify what needs to change (from JUNO's assignment)
+    2. Verify correct value in codebase (read .env, source files, config)
+    3. Document verification in task (which files read, what found)
+    4. Use Read tool BEFORE making changes
+    5. Use Edit tool with verified information only
+    6. DO NOT make assumptions or guesses
+  - **Verification examples:**
+    - API ports → Read .env, server.js, app.js
+    - Table names → Read init.sql or check production database
+    - Endpoint URLs → Read route files
+    - Method signatures → Read actual source file
+    - Configuration values → Read config files
+  - **Documentation format:**
+
+    ```markdown
+    - [x] docs/api/README.md
+      - Verification: Read backend/.env - confirmed port is 3001
+      - Changes made: Updated 49 instances of port number to 3001
+    ```
+
+- **Trinity-docs-update - JUNO verification loop** - Phase 3 ensures 100% completion
+  before final audit
+  - **Step 3.1:** JUNO checks all three APO checklists for completion status
+    - Counts total tasks vs completed tasks per APO
+    - Calculates completion percentage
+    - Determines next action (PROCEED or RESTART)
+  - **Step 3.1A:** Re-launch incomplete APOs automatically
+    - Identifies incomplete APOs from JUNO's report
+    - Restarts only incomplete APOs with resume instructions
+    - Loops until all APOs reach 100%
+  - **Step 3.2:** JUNO final quality audit (only when all APOs 100% complete)
+    - Verifies files created/updated
+    - Checks content accuracy against codebase
+    - Validates no hallucinated components
+    - Generates verification report with pass/fail status
+  - **Output:** `trinity/reports/DOCS-UPDATE-VERIFICATION-{{DATE}}.md`
+
+- **Trinity-docs-update - Three template files** - Command template and two checklist
+  templates deployed via CLI
+  - **Command Template:**
+    `src/templates/.claude/commands/maintenance/trinity-docs-update.md.template`
+    - Deployed to: `.claude/commands/maintenance/trinity-docs-update.md`
+    - Updated by: `trinity update` command via `updateCommands()` function
+  - **JUNO Checklist:**
+    `src/templates/trinity/templates/documentation/reports/juno-docs-update-checklist.md.template`
+    - Deployed to:
+      `trinity/templates/documentation/reports/juno-docs-update-checklist.md`
+    - Updated by: `trinity update` command via `updateTemplates()` function (recursively
+      copies all documentation templates)
+  - **APO Checklist:**
+    `src/templates/trinity/templates/documentation/reports/apo-docs-update-checklist.md.template`
+    - Deployed to:
+      `trinity/templates/documentation/reports/apo-docs-update-checklist.md`
+    - Updated by: `trinity update` command via `updateTemplates()` function (recursively
+      copies all documentation templates)
+  - All templates automatically deployed during `trinity deploy` and updated during
+    `trinity update`
+
+- **Trinity-docs command - Complete architectural overhaul** - Transformed from
+  single-agent to multi-agent orchestration
+  - **New Architecture:** JUNO audit → 3 parallel APO instances → Verification
+  - **JUNO Agent Integration:** Read-only codebase audit creates documentation checklist
+    before generation
+  - **Parallel APO Execution:** APO-1 (diagrams), APO-2 (guides/API), APO-3 (config) run
+    concurrently
+  - **Performance:** 3x faster execution via parallel agent orchestration
+  - **Context Efficiency:** Each agent receives focused instructions (<100 lines) vs
+    single 2,577-line spec
+
+- **Trinity-docs command - External template system** - Created 28 reusable documentation
+  templates
+  - **Template Directory:** `trinity/templates/documentation/` with 8 categories
+  - **Mermaid Diagrams (4 templates):** MVC flow, database ER, API endpoint map,
+    component hierarchy
+  - **Guides (4 templates):** Getting started, API development, deployment, contributing
+  - **API Documentation (1 template):** API README with endpoint structure
+  - **Configuration (2 templates):** Documentation structure, env-example generator
+  - **Discovery (4 templates):** Framework detection, component discovery, API endpoint
+    scanner, env variable extraction
+  - **Validation (3 templates):** APO self-validation checklists for all 3 agents
+  - **Processes (6 templates):** APO workflows (common, diagram-specific,
+    guide-specific, config-specific), error handling, fallback mechanisms
+  - **Reports (2 templates):** JUNO internal report, ROOT-README for template organization
+  - **Template Variables:** All templates use `{{UPPERCASE_UNDERSCORE}}` syntax for
+    dynamic content replacement
+
+- **Trinity-docs command - Template validation phase** - Optional Phase 0.2 validates
+  template syntax
+  - Validates `{{VARIABLE}}` syntax (must be UPPERCASE_UNDERSCORE)
+  - Detects nested variables (not supported)
+  - Checks balanced braces
+  - Non-blocking warnings for template issues
+
+- **Trinity-docs command - Retry mechanism** - Phase 0.25 handles transient failures
+  - Retries operations up to 3 times with 500ms delay
+  - Handles filesystem delays and race conditions
+  - Graceful degradation for non-critical operations
+
+- **Trinity-docs command - JUNO documentation audit** - Phase 1 performs comprehensive
+  codebase analysis
+  - **Framework Detection:** Analyzes package.json for Express, NestJS, React, Next.js,
+    Django, Flask, FastAPI
+  - **Component Discovery:** Scans for React/Vue/Angular/Svelte components with
+    zero-tolerance for fake components
+  - **API Endpoint Scanning:** Detects Express/Fastify/NestJS/Koa routes with enhanced
+    patterns
+  - **Database Detection:** PostgreSQL, MySQL, MongoDB, SQLite, Redis via dependency
+    analysis
+  - **Environment Variables:** Extracts from .env and process.env usage patterns
+  - **Checklist Report:** Generates
+    `trinity/templates/documentation/reports/juno-internal-report.md` with all discovered
+    metadata
+
+- **Trinity-docs command - Fallback mechanism** - Handles missing JUNO data gracefully
+  - Uses discovery templates when JUNO variables missing
+  - Framework detection fallback via package.json analysis
+  - Component discovery fallback for frontend frameworks
+  - API endpoint scanner fallback for backend frameworks
+  - Environment variable extraction fallback
+  - Default template paths when discovery fails
+
+- **Trinity-docs command - APO self-validation** - Each APO validates its own work before
+  completion
+  - APO-1 validates: 4 diagram files created, correct paths, no placeholders, proper
+    Mermaid syntax
+  - APO-2 validates: Guide completeness, API documentation accuracy, no fake examples
+  - APO-3 validates: Config files exist, no hardcoded secrets, proper .env.example format
+  - Security checks for APO-3: No API keys, passwords, tokens, or sensitive data in
+    generated files
+
+- **Trinity-docs command - Enhanced verification phase** - Phase 4 performs comprehensive
+  quality checks
+  - Verifies all JUNO checklist items completed
+  - Validates file existence and content quality
+  - Checks for placeholders and fake data
+  - Ensures proper Mermaid syntax in diagrams
+  - Validates security (no secrets in config files)
+  - Generates final completion report with pass/fail status
+
+### Changed
+
+- **Trinity-docs command - File relocation** - Moved from
+  `src/templates/shared/claude-commands/` to
+  `src/templates/.claude/commands/execution/`
+  - Aligns with new command categorization structure
+  - Distinguishes execution commands from utility/session/planning commands
+
+- **Trinity-docs command - Diagram output path** - Changed from
+  `docs/architecture/diagrams/` to `docs/architecture/`
+  - Simplified directory structure
+  - All architecture files (diagrams, overview, ADRs) now in single directory
+  - Updated all references throughout command specification (lines 1079, 1205-1208)
+
+- **Trinity-docs command - API endpoint scanner enhancement** - Added 3 missing route
+  detection patterns
+  - Added `router.route('...').get|post|put|patch|delete()` pattern
+  - Added `app.route('...').get|post|put|patch|delete()` pattern
+  - Added `router.all('...')` wildcard route pattern
+  - Fixes endpoint count variance (33 vs 34 detected endpoints)
+
+- **Trinity-docs command - Configuration directory consolidation** - Merged `config/` into
+  `configuration/`
+  - Moved `env-example-generator.md.template` from `config/` to `configuration/`
+  - Removed duplicate directory structure
+  - Now single `configuration/` directory with 2 templates
+
+- **Trinity-docs command - Version update** - Updated to v2.0.9
+  - Reflects architectural overhaul and template externalization
+  - Command now references 28 external templates vs inline logic
+
+### Deprecated
+
+### Removed
+
+- **Trinity-docs command - Inline documentation logic** - Removed 808+ lines of inline
+  instructions (WO-004)
+  - Phase 1 codebase analysis logic → `trinity/templates/documentation/discovery/`
+    templates
+  - Phase 2 content seeding → `trinity/templates/documentation/guides/` templates
+  - Diagram generation → `trinity/templates/documentation/mermaid-diagrams/` templates
+  - Validation logic → `trinity/templates/documentation/validation/` templates
+
+- **Trinity-docs command - Single-agent architecture** - Replaced with multi-agent
+  orchestration
+  - Old: Single APO reads 2,577-line spec and performs all work
+  - New: JUNO audit + 3 parallel APO instances with focused instructions
+  - Reduces context fatigue and improves reliability
+
+### Fixed
+
+### Security
+
+## [2.0.9] - 2026-01-12
+
+### Changed
+
+- **Trinity-docs command specification** - Added evidence-based documentation verification
+  - Added Rule 2: Evidence-Based Documentation Only - prevents documenting uninstalled
+    tools
+  - Added Phase 1 Step 6: Tool & Feature Verification for all project types
+  - Added tool verification report to Phase 5 output
+  - Prevents aspirational/best-practice content that doesn't exist in codebase
+  - Addresses incident where Lighthouse was documented without being installed
+
+- **Trinity-readme command specification** - Removed Trinity self-documentation conflicts
+  - Deleted Type C Template that documented Trinity infrastructure (violated Rule 1)
+  - Added Rule 1 Enforcement Checklist with verification commands
+  - Added Phase 1 Step 4.5: Filter Gitignored and Trinity Directories
+  - Added Trinity Detection Warning to explicitly skip trinity/ and .claude/
+  - Removed trinity/ from glob patterns and project structure examples
+  - Addresses incident where trinity/ was included in README file tree despite being
+    gitignored
+
+- **Trinity-readme command specification** - Added LICENSE file verification for badges
+  - Added Phase 1 Step 7: License Verification - reads actual LICENSE file
+  - LICENSE file is now source of truth (priority over package.json)
+  - Detects license type from file header (MIT, ISC, Apache, GPL, BSD, etc.)
+  - Warns when package.json license field doesn't match LICENSE file
+  - Falls back to package.json only if LICENSE file doesn't exist
+  - Addresses incident where ISC badge was generated despite MIT LICENSE file
+
+- **Trinity-docs command specification** - Added Trinity reference sanitization enforcement
+  - Added Rule 1 Forbidden Patterns - explicit list of patterns that must not appear in
+    docs/
+  - Added Phase 4.5: Trinity Reference Sanitization - scans and removes Trinity references
+  - Added Rule 1 Compliance verification to Phase 5 report with pass/fail status
+  - Removed Trinity report link from docs/README.md template footer
+  - Prevents Trinity Method, agent names, commands, and infrastructure references in user
+    docs
+  - Addresses incident where 7 documentation files contained Trinity Method references
+
+## [2.0.8] - 2026-01-08
+
+### Added
+
+- **Bot directory support** - Added `bot/` as a recognized source directory
+  - `bot/` directory now detected during deployment
+  - Framework-specific CLAUDE.md automatically deployed to `bot/` directory
+  - Supports nested patterns: `bot/src`, `bot/lib`, `bot/app`, `src/bot`
+
+- **Force update flag** - Added `--force` flag to `trinity update` command
+  - Allows forcing re-update even when already at latest version
+  - Useful for repairing corrupted deployments or applying template fixes
+  - Usage: `trinity update --force`
+
+## [2.0.7] - 2026-01-06
+
+### Fixed
+
+- **CRITICAL: Agent file extension handling** - Fixed agent updates to strip `.template`
+  extension
+  - Agents were being copied with `.md.template` extension, creating duplicates alongside
+    old `.md` files
+  - Now correctly strips `.template` extension during deployment to `.claude/agents/`
+    subdirectories
+  - Each agent file copied individually with proper extension handling
+
+- **CRITICAL: Template directory structure** - Fixed template updates to use correct
+  directory structure
+  - Work order templates were being deployed to wrong directory (`trinity/templates/`
+    instead of `trinity/templates/work-orders/`)
+  - Documentation templates (`trinity/templates/documentation/`) were not being updated at
+    all
+  - Investigation templates (`trinity/templates/investigations/`) were not being updated
+    at all
+  - Now correctly deploys all 3 template types to their proper subdirectories with
+    `.template` extension stripped
+  - Total templates updated: 13 files (6 work-orders + 2 documentation + 5 investigations)
+
+## [2.0.6] - 2026-01-06
+
+### Fixed
+
+- **CRITICAL: Command categorization logic** - Fixed `trinity update` to correctly
+  categorize slash commands
+  - Execution commands (`audit`, `changelog`, `docs`, `readme`) were falling through to
+    utility category
+  - Investigation commands containing `investigate` were not being matched properly
+  - Commands now deploy to correct category directories (session, planning, execution,
+    investigation, infrastructure, infrastructure, utility)
+  - Prevents duplicate commands in wrong directories during updates
+
+## [2.0.5] - 2026-01-06
+
+### Fixed
+
+- **CRITICAL: Slash command file updates** - Fixed `trinity update` command file extension
+  handling
+  - Update commands module was looking for `.md` files but templates use `.md.template`
+    extension
+  - Now correctly processes `.md.template` files and strips extension for deployed files
+  - Slash commands now update properly (20 command files) when running `trinity update`
+  - Matches the pattern used by knowledge-base update module
+
+## [2.0.4] - 2026-01-06
+
+### Fixed
+
+- **CRITICAL: Update command path resolution** - Fixed `trinity update` to use centralized
+  SDK path resolution
+  - Update command was using hardcoded `@trinity-method/sdk` path instead of
+    `trinity-method-sdk`
+  - Commands, agents, templates, and knowledge base files now update correctly with global
+    installations
+  - Fixed "Commands template path not found, skipping" warning
+
+## [2.0.3] - 2026-01-06
+
+### Fixed
+
+- **CRITICAL: Global install support** - Fixed SDK path resolution to work with global
+  installations
+  - Changed package name from incorrect `@trinity-method/sdk` to `trinity-method-sdk` in
+    path resolution
+  - Added `import.meta.url` support for resolving SDK location in global installs
+  - `trinity update` command now works correctly when SDK is installed globally
+  - Fixed "ENOENT: no such file or directory" error when running update command
+
+## [2.0.2] - 2026-01-02
+
+### Added
+
+- **DOCUMENTATION RULES** section to all APO documentation commands (`/trinity-docs`,
+  `/trinity-readme`, `/trinity-changelog`)
+  - Rule 1: No Self-Serving Trinity Documentation - Prevents APO from including Trinity
+    Method information in user project documentation
+  - Provides clear examples and rationale for focusing exclusively on user's codebase
+- Explicit **Write tool execution commands** throughout `/trinity-docs` Phase 2
+  - Added CRITICAL EXECUTION REQUIREMENT section at Phase 2 start
+  - Added **EXECUTION REQUIRED** code blocks for each seeding step
+  - Added **Phase 2 Execution Summary** with mandatory file creation checklist
+  - Ensures APO creates actual documentation files instead of just showing templates
+
+### Changed
+
+- **`/trinity-docs` command:** Enhanced Phase 2 with explicit Write tool requirements
+  - Step 2 (Guides): Added execution requirements for getting-started.md and
+    framework-specific guides
+  - Step 3 (API): Added execution requirements for api/README.md
+  - Step 4 (Architecture): Added execution requirements for architecture/overview.md
+  - Step 5 (Reference): Added execution requirements for reference/README.md
+  - Phase now requires minimum 4 files to be created: getting-started.md, api/README.md,
+    architecture/overview.md, reference/README.md
+
+### Fixed
+
+- **APO file creation issue:** `/trinity-docs` now explicitly commands APO to use Write
+  tool, preventing scenario where directory structure is created but documentation files
+  are not written
+
+## [2.0.1] - 2025-12-29
+
+### Added
+
+- Installation instructions in README.md with npx and global install options
+- Automatic npm deployment on every push to main branch via GitHub Actions CD workflow
+
+### Changed
+
+- **CD Workflow:** Modified to deploy to npm on all main branch pushes (not just version
+  tags)
+- **CD Workflow:** GitHub releases now only created for version tags, not regular commits
+- Updated all package references from `@trinity-method/cli` to `trinity-method-sdk`
+
+### Fixed
+
+- Removed redundant `node_modules/` from Trinity's .gitignore additions
+
+## [2.0.0] - 2025-12-21
+
+### Added
+
+- **Agent System Expansion:** Grew from 7 to 19 specialized agents
+  - **Planning Layer (4 agents):** MON (Requirements Analyst), ROR (Design Architect),
+    TRA (Work Planner), EUS (Task Decomposer)
+  - **Execution Layer (3 agents):** KIL (Task Executor), BAS (Quality Gate),
+    DRA (Code Reviewer)
+  - **Support Layer (4 agents):** APO (Documentation Specialist),
+    BON (Dependency Manager), CAP (Configuration Specialist),
+    URO (Refactoring Specialist)
+  - **Leadership & Audit (2 agents):** ALY (Chief Technology Officer),
+    JUNO (Quality Auditor)
+  - **Infrastructure (5 agents):** TAN, ZEN, INO, EIN, AJ MAESTRO (legacy)
+- Increased deployment from 49 to 64 production-ready components
+- Expanded slash commands from 8 to 20 commands across 6 categories
+  - Session Management: `/trinity-start`, `/trinity-continue`, `/trinity-end`
+  - Planning: `/trinity-requirements`, `/trinity-design`, `/trinity-decompose`,
+    `/trinity-plan`
+  - Execution: `/trinity-orchestrate`, `/trinity-audit`, `/trinity-readme`,
+    `/trinity-docs`, `/trinity-changelog`
+  - Investigation: `/trinity-create-investigation`, `/trinity-plan-investigation`,
+    `/trinity-investigate-templates`
+  - Infrastructure: `/trinity-init`
+  - Utility: `/trinity-verify`, `/trinity-agents`, `/trinity-workorder`
+- Enhanced `/trinity-readme` command template to v2.0.0 with comprehensive validation
+  phases
+  - Phase 2h: Command/Script/CLI Validation - Verifies all documented commands exist in
+    codebase
+  - Phase 2i: Code Example Validation - Checks code examples match current API signatures
+  - Phase 2j: API/Function Reference Validation - Verifies documented functions/classes
+    exist
+  - Phase 2k: Dependency Claims Validation - Cross-references README with package
+    manifests
+  - Phase 2l: Stale Content Detection - Finds TODO markers, outdated dates, placeholder
+    text
+
+### Changed
+
+- **BREAKING:** Updated Trinity Method to v2.0.0 architecture
+- **Agent System:** Complete agent architecture redesign with specialized layers
+- **Documentation System:** Enhanced APO capabilities with comprehensive audit phases
+- Refactored 7 functions to reduce cyclomatic complexity (all ≤15)
+- Improved code maintainability and readability across codebase
+- Enhanced test coverage and reliability (405 tests, 100% passing)
+
+### Deprecated
+
+- AJ MAESTRO orchestrator (v1.0) replaced by ALY in v2.0
+
+### Fixed
+
+- Template path resolution in integration tests
+- Linting deployment tests now correctly locate template files
+- **Documentation Accuracy:** Fixed 6 critical inaccuracies in README.md
+  - Removed 24+ non-existent CLI commands (`npx trinity investigate`, `crisis`,
+    `analytics`, etc.)
+  - Fixed 13 broken documentation links (docs/methodology/, docs/adr/, docs/workflows/)
+  - Corrected agent count inconsistencies throughout documentation (unified to 18 agents)
+  - Updated deployment examples to reflect actual CLI
+    (`npx @trinity-method/cli deploy/update`)
+- Fixed broken ADR links in src/README.md (replaced with design principles summary)
+- Fixed broken ADR links in docs/README.md (removed non-existent file references)
+
+---
+
+## [1.0.1] - 2025-10-02 (Legacy - @trinity-method/cli)
+
+### Fixed
+
+- **Critical:** Missing template files in npm package (only 9 of 36 were included)
+- Fixed file paths to use bundled templates instead of workspace structure
+- All `.md.template` files now properly included in published package
+- Updated `deploy.js` and `update.js` to reference correct template locations
+- Bundled agents and hooks directly into CLI package for standalone operation
+
+### Changed
+
+- Reorganized package structure to be self-contained when published to npm
+- Templates, agents, and hooks now bundled in `packages/cli/templates/`
+
+**Note:** This version was published as `@trinity-method/cli`. Starting with v2.0.0,
+the package was renamed to `trinity-method-sdk`.
+
+---
+
+## [1.0.0] - 2025-10-01 (Legacy - @trinity-method/cli)
+
+### Added
+
+- Initial release of Trinity Method SDK for Claude Code
+- 7 specialized Trinity agents (Aly, AJ, TAN, ZEN, INO, Ein, JUNO)
+- Claude Code-exclusive deployment
+- Interactive deployment with linting and CI/CD configuration
+- Linting configuration (ESLint, Prettier, etc.)
+- CI/CD automation (GitHub Actions, GitLab CI)
+- Matrix testing support
+- Coverage integration (Codecov, Coveralls)
+- Employee Directory with agent documentation
+- Trinity structure (knowledge-base, templates)
+- CLAUDE.md context file deployment
+- README injection for Trinity Method section
+- 8 slash commands (/trinity-init, /trinity-verify, /trinity-docs, /trinity-start,
+  /trinity-continue, /trinity-end, /trinity-workorder, /trinity-agents)
+- Session management with archival system
+- Comprehensive CLI documentation
+
+### Strategic Decision
+
+- Focused exclusively on Claude Code for exceptional user experience
+- Community contributions welcome for other coding agents
+
+**Note:** This version was published as `@trinity-method/cli`. Starting with v2.0.0,
+the package was renamed to `trinity-method-sdk`.
+
+[1.0.0]: https://github.com/lukadfagundes/trinity-method-sdk/releases/tag/v1.0.0