trinity-method-sdk 2.1.0 → 2.2.1

package/dist/templates/trinity/CLAUDE.md.template

@@ -39,7 +39,7 @@
 ### Session Initialization
 ```markdown
 ## Required Steps at Session Start:
-1. Load project context from ../CLAUDE.md
+1. Load project context from ../../CLAUDE.md
 2. Review outstanding tasks in knowledge-base/To-do.md
 3. Check system health and performance metrics
 4. Update dependencies if needed
@@ -63,7 +63,7 @@
 ### Session Artifacts Management
 ```yaml
 Session Artifacts:
-  Location: trinity/sessions/[YYYY-MM-DD]-[HHMMSS]/
+  Location: .claude/trinity/sessions/[YYYY-MM-DD]-[HHMMSS]/
   Required Files:
     - SESSION-SUMMARY.md         # Session overview and accomplishments
     - investigation-summary.md   # What was investigated
@@ -94,7 +94,7 @@ Session Artifacts:
 ```markdown
 ## Response for Performance Degradation:
 1. Measure current performance metrics
-2. Compare against established baselines in ../CLAUDE.md
+2. Compare against established baselines in ../../CLAUDE.md
 3. Identify performance bottlenecks
 4. Investigate using Trinity methodology
 5. Implement targeted optimizations
@@ -237,14 +237,14 @@ const trinityMetrics = {
 ### Knowledge Persistence Framework
 ```yaml
 Knowledge Base Structure:
-  trinity/knowledge-base/
+  .claude/trinity/knowledge-base/
     - ISSUES.md              # Common problems and solutions
     - Trinity.md             # Trinity Method project guide
     - ARCHITECTURE.md        # System architecture documentation
     - Technical-Debt.md      # Technical debt tracking
     - To-do.md               # Task tracking and planning
 
-  trinity/sessions/
+  .claude/trinity/sessions/
     - [YYYY-MM-DD]-[HHMMSS]/  # Session artifacts
       - SESSION-SUMMARY.md
       - investigation-summary.md
@@ -252,13 +252,13 @@ Knowledge Base Structure:
       - issues-resolved.md
       - performance-report.md
 
-  trinity/investigations/
+  .claude/trinity/investigations/
     - [investigation-name]/    # Investigation work products
 
-  trinity/patterns/
+  .claude/trinity/patterns/
     - [pattern-name].md        # Reusable solution patterns
 
-  trinity/work-orders/
+  .claude/trinity/work-orders/
     - WORKORDER-XXX.md         # Active work orders
 ```
 
@@ -326,9 +326,9 @@ Execute Framework Crisis Protocol
 
 ### Hierarchical Context Loading
 ```
-1. ../CLAUDE.md              → Global project context (load FIRST)
-2. trinity/CLAUDE.md (this file) → Trinity Method enforcement (load SECOND)
-3. ../{{SOURCE_DIR}}/CLAUDE.md   → Technology-specific rules (load THIRD)
+1. ../../CLAUDE.md              → Global project context (load FIRST)
+2. .claude/trinity/CLAUDE.md (this file) → Trinity Method enforcement (load SECOND)
+3. ../../{{SOURCE_DIR}}/CLAUDE.md   → Technology-specific rules (load THIRD)
 ```
 
 ### Context Priority Rules
@@ -341,7 +341,7 @@ Execute Framework Crisis Protocol
 
 ## Reference to Parent Context
 
-This file extends and enforces the global requirements defined in `../CLAUDE.md`. All Trinity Method protocols must comply with:
+This file extends and enforces the global requirements defined in `../../CLAUDE.md`. All Trinity Method protocols must comply with:
 - Global performance baselines
 - Project-wide behavioral requirements
 - Technology stack specifications
@@ -355,10 +355,10 @@ For technology-specific implementation details, see: `../src/CLAUDE.md`
 
 This file enforces Trinity Method protocols for all development work.
 
-**Parent Context**: [../CLAUDE.md](../CLAUDE.md) - Project overview and global requirements
+**Parent Context**: [../../CLAUDE.md](../../CLAUDE.md) - Project overview and global requirements
 **Child Context**: [../src/CLAUDE.md](../src/CLAUDE.md) - Framework-specific implementation rules
 **Related Resources**:
-- [Agent Directory](../.claude/EMPLOYEE-DIRECTORY.md) - 19-agent Trinity team guide
+- [Agent Directory](../EMPLOYEE-DIRECTORY.md) - 19-agent Trinity team guide
 - [Architecture Documentation](knowledge-base/ARCHITECTURE.md) - System architecture and patterns
 - [Known Issues](knowledge-base/ISSUES.md) - Issue patterns and resolutions
 - [Technical Debt](knowledge-base/Technical-Debt.md) - Debt tracking and reduction plans

package/dist/templates/trinity/knowledge-base/ARCHITECTURE.md.template

@@ -27,7 +27,7 @@ const {{PROJECT_VAR_NAME}}Stack = {
 ```
 {{PROJECT_NAME}}/
 ├── {{SOURCE_DIR}}/              # Main source code
-├── trinity/                     # Trinity Method implementation
+├── .claude/trinity/                     # Trinity Method implementation
 │   ├── knowledge-base/         # Architecture & documentation
 ├── tests/                      # Test suites
 └── docs/                       # Additional documentation
@@ -308,9 +308,9 @@ graph LR
 
 ### Knowledge Capture
 - Architecture decisions recorded here
-- Patterns documented in trinity/patterns/
-- Issues tracked in trinity/knowledge-base/ISSUES.md
-- Sessions archived in trinity/sessions/
+- Patterns documented in .claude/trinity/patterns/
+- Issues tracked in .claude/trinity/knowledge-base/ISSUES.md
+- Sessions archived in .claude/trinity/sessions/
 
 ---
 

package/dist/templates/trinity/knowledge-base/ISSUES.md.template

@@ -225,8 +225,8 @@ Pattern_Prevention_Rate: {{PERCENTAGE}}%
    - Dependencies: {{DEPENDENCIES}}
 
 ### Completed Investigations (This Session)
-- [x] {{COMPLETED_1}} - See: trinity/investigations/{{DATE}}-{{INVESTIGATION}}.md
-- [x] {{COMPLETED_2}} - See: trinity/investigations/{{DATE}}-{{INVESTIGATION}}.md
+- [x] {{COMPLETED_1}} - See: .claude/trinity/investigations/{{DATE}}-{{INVESTIGATION}}.md
+- [x] {{COMPLETED_2}} - See: .claude/trinity/investigations/{{DATE}}-{{INVESTIGATION}}.md
 
 ---
 
@@ -285,7 +285,7 @@ Solution:
 
 Prevention:
   Pattern_Created: {{YES/NO}}
-  Pattern_Location: trinity/patterns/{{PATTERN_FILE}}
+  Pattern_Location: .claude/trinity/patterns/{{PATTERN_FILE}}
   Guidelines_Updated: {{YES/NO}}
 
 Metrics:
@@ -346,7 +346,7 @@ Metrics:
 - **ARCHITECTURE.md**: System design and components
 - **Trinity.md**: Methodology implementation
 - **To-do.md**: Pending fixes and improvements
-- **Pattern Library**: trinity/patterns/
+- **Pattern Library**: .claude/trinity/patterns/
 
 ---
 
@@ -417,7 +417,7 @@ Updates_Required:
   - Active_Issues: Add new issue with P0/P1/P2/P3 priority
   - Issue_Template: Fill with symptoms, root cause, solution
   - Pattern_Check: Is this a recurring issue? Create pattern if yes
-  - Investigation_Link: Link to trinity/investigations/ file if investigation done
+  - Investigation_Link: Link to .claude/trinity/investigations/ file if investigation done
   - Cross_References:
     - To-do.md: Add fix task with priority
     - Technical-Debt.md: Add debt if issue reveals shortcuts
@@ -442,7 +442,7 @@ Updates_Required:
   - Pattern_Frequency: Update occurrence count
   - Related_Issues: Link all issue IDs that match this pattern
   - Prevention_Measures: Document how to prevent this pattern
-  - Pattern_Library: Create pattern file in trinity/patterns/
+  - Pattern_Library: Create pattern file in .claude/trinity/patterns/
   - Cross_References:
     - Technical-Debt.md: Link pattern to debt if applicable
     - CODING-PRINCIPLES.md: Add principle if pattern reveals standard gap
@@ -481,7 +481,7 @@ Updates_Required:
 4. **Link Investigation**: If investigation file exists, link it
 5. **Update Metrics**: Increment counts, update averages
 6. **Cross-Reference**: Update related documents (To-do, Technical-Debt, etc.)
-7. **Pattern Library**: Create trinity/patterns/ file if reusable solution
+7. **Pattern Library**: Create .claude/trinity/patterns/ file if reusable solution
 8. **Update Timestamp**: Set `**Last Updated**: {{CURRENT_DATE}}` to actual date
 
 **Quality Checklist:**
@@ -530,7 +530,7 @@ Updates_Required:
 **Update Frequency**: Real-time (as issues discovered) + session-based
 **Maintained By**: Development team using Trinity Method
 **Referenced By**: `/trinity-end` command for session updates
-**Pattern Library**: Creates trinity/patterns/ files
+**Pattern Library**: Creates .claude/trinity/patterns/ files
 **Last Updated**: {{CURRENT_DATE}}
 
 ---

package/dist/templates/trinity/knowledge-base/Technical-Debt.md.template

@@ -402,8 +402,6 @@ const calculateDebtScore = () => {
 - **ARCHITECTURE.md**: System design decisions
 - **Trinity.md**: Methodology implementation
 - **To-do.md**: Actionable task list
-- **Pattern Library**: trinity/patterns/
-
 ---
 
 ## 📝 WHEN TO UPDATE THIS DOCUMENT
@@ -512,7 +510,7 @@ Updates_Required:
   - Debt_Reduction_Plan: Add to Quick Wins or Strategic Improvements
   - Cross_References:
     - ISSUES.md: Link to duplication pattern if causes issues
-    - trinity/patterns/: Create pattern file
+    - Document pattern in Pattern Library section above
 ```
 
 **Scenario: Security Vulnerability Fixed**

package/dist/templates/trinity/knowledge-base/To-do.md.template

@@ -29,7 +29,7 @@
 ### Feature Development
 - [ ] **{{FEATURE_1}}**
   - Investigation Required: YES
-  - Pattern Check: trinity/patterns/
+  - Pattern Check: Technical-Debt.md#pattern-library
   - Tests Required: Unit + Integration
   - Documentation: Update ARCHITECTURE.md
   - Estimated: {{TIME_ESTIMATE}}

package/dist/templates/trinity/knowledge-base/Trinity.md.template

@@ -30,12 +30,12 @@ Every feature/fix in {{PROJECT_NAME}} requires investigation:
    - Security considerations
 
 3. **Pattern Discovery** (5 minutes)
-   - Check trinity/patterns/ for existing solutions
+   - Check .claude/trinity/patterns/ for existing solutions
    - Document new patterns if discovered
    - Update pattern library
 
 4. **Documentation** (5 minutes)
-   - Save to trinity/investigations/[date]-[feature].md
+   - Save to .claude/trinity/investigations/[date]-[feature].md
    - Update relevant knowledge base files
    - Link to issues if applicable
 
@@ -103,7 +103,7 @@ Debug_Levels:
 
 ### Pre-Implementation Checklist
 - [ ] Investigation completed
-- [ ] Existing patterns reviewed (trinity/patterns/)
+- [ ] Existing patterns reviewed (.claude/trinity/patterns/)
 - [ ] Performance impact assessed
 - [ ] Security implications considered
 - [ ] Test plan created
@@ -233,7 +233,7 @@ Session_End:
     - Update metrics
 
   3_Archive:
-    - Move to trinity/sessions/[date]/
+    - Move to .claude/trinity/sessions/[date]/
     - Create session summary
     - Update project metrics
     - Plan next session
@@ -245,7 +245,7 @@ Session_End:
 
 ### Pattern Discovery Process
 1. **Identify**: Recognize recurring solutions
-2. **Document**: Create pattern file in trinity/patterns/
+2. **Document**: Create pattern file in .claude/trinity/patterns/
 3. **Validate**: Test pattern effectiveness
 4. **Share**: Update pattern index
 5. **Reuse**: Apply in future implementations

package/dist/templates/trinity/templates/documentation/configuration/env-example-generator.md.template

@@ -326,7 +326,7 @@ APO-3 will receive these pre-filled variables from JUNO's audit report:
 ```markdown
 ## File 1: .env.example
 
-**Template:** trinity/templates/documentation/config/env-example-generator.md.template
+**Template:** .claude/trinity/templates/documentation/config/env-example-generator.md.template
 
 **Variables to Replace:**
 - {{PROJECT_NAME}}: "dnd-tool"

package/dist/templates/trinity/templates/documentation/processes/error-handling-protocol.md.template

@@ -107,7 +107,7 @@ Details: [ADDITIONAL_INFO]
 
 **Tier 1 (ABORT):**
 - Cannot read JUNO report from global state
-- Cannot read guide templates from trinity/templates/documentation/
+- Cannot read guide templates from .claude/trinity/templates/documentation/
 - Cannot write guide files (permission denied)
 
 **Tier 2 (WARN):**
@@ -149,7 +149,7 @@ if (juno_incomplete || data_missing) {
   LOG: `Reason: ${fallback_reason}`;
 
   // Use discovery templates directly
-  // See trinity/templates/discovery/ for patterns
+  // See .claude/trinity/templates/discovery/ for patterns
 
   // Mark fallback usage
   fallback_used = true;

package/dist/templates/trinity/templates/documentation/reports/apo-docs-update-checklist.md.template

@@ -11,14 +11,14 @@
 
 ```
 Use Task tool with subagent_type="APO (Documentation Specialist)" to write:
-- File path: trinity/reports/apo-{{DESIGNATION}}-docs-update-checklist.md
+- File path: .claude/trinity/reports/apo-{{DESIGNATION}}-docs-update-checklist.md
 - Content: Copy of this template
 ```
 
 **Example file paths:**
-- APO-1: `trinity/reports/apo-1-docs-update-checklist.md`
-- APO-2: `trinity/reports/apo-2-docs-update-checklist.md`
-- APO-3: `trinity/reports/apo-3-docs-update-checklist.md`
+- APO-1: `.claude/trinity/reports/apo-1-docs-update-checklist.md`
+- APO-2: `.claude/trinity/reports/apo-2-docs-update-checklist.md`
+- APO-3: `.claude/trinity/reports/apo-3-docs-update-checklist.md`
 
 **You MUST use Task skill Write to create your checklist file before proceeding.**
 
@@ -29,7 +29,7 @@ Use Task tool with subagent_type="APO (Documentation Specialist)" to write:
 1. **Use Task skill Read to read JUNO's audit report:**
    ```
    Use Task tool with subagent_type="APO (Documentation Specialist)" to read:
-   - File path: trinity/reports/DOCS-UPDATE-AUDIT-{{DATE}}.md
+   - File path: .claude/trinity/reports/DOCS-UPDATE-AUDIT-{{DATE}}.md
    ```
 
 2. **Find your section:**
@@ -68,7 +68,7 @@ Use Task tool with subagent_type="APO (Documentation Specialist)" to write:
 1. **Start with the first unchecked task** on your list
 2. **Complete the task** (create or update the documentation file using Task skill)
 3. **Update your checklist** - Mark the task as complete: `- [x]`
-4. **Use Task skill Edit to save your updated checklist** to `trinity/reports/apo-{{DESIGNATION}}-docs-update-checklist.md`
+4. **Use Task skill Edit to save your updated checklist** to `.claude/trinity/reports/apo-{{DESIGNATION}}-docs-update-checklist.md`
 5. **Move to the next task** and repeat
 
 **DO NOT:**
@@ -298,7 +298,7 @@ import ComponentName from './ComponentName';
 1.  All tasks on your checklist are marked `- [x]`
 2.  All documentation files created/updated
 3.  All files saved to correct locations
-4.  Your checklist saved to `trinity/reports/apo-{{DESIGNATION}}-docs-update-checklist.md`
+4.  Your checklist saved to `.claude/trinity/reports/apo-{{DESIGNATION}}-docs-update-checklist.md`
 
 **Once all tasks complete:**
 - Report completion

package/dist/templates/trinity/templates/documentation/reports/juno-docs-update-checklist.md.template

@@ -2,7 +2,7 @@
 
 **Purpose:** Comprehensive audit checklist for trinity-docs-update command
 **Agent:** JUNO (Quality Auditor)
-**Output:** Audit report saved to `trinity/reports/DOCS-UPDATE-AUDIT-{{DATE}}.md`
+**Output:** Audit report saved to `.claude/trinity/reports/DOCS-UPDATE-AUDIT-{{DATE}}.md`
 
 ---
 
@@ -835,7 +835,7 @@ When assigning frontend modules to APO-3:
 
 ## Step 1.4: Generate 3-Part Audit Report
 
-**Use template:** `trinity/templates/documentation/reports/docs-update-audit.md`
+**Use template:** `.claude/trinity/templates/documentation/reports/docs-update-audit.md`
 
 ### Part 1: Base Documentation Updates Needed
 
@@ -1308,7 +1308,7 @@ Aborting documentation update.
 
 ```
 Use Task tool with subagent_type="APO (Documentation Specialist)" to write the file:
-- File path: trinity/reports/DOCS-UPDATE-AUDIT-{{DATE}}.md
+- File path: .claude/trinity/reports/DOCS-UPDATE-AUDIT-{{DATE}}.md
 - Content: Complete audit report with all sections above
 ```
 
@@ -1328,7 +1328,7 @@ Use Task tool with subagent_type="APO (Documentation Specialist)" to write the f
 Once audit is complete:
 1. ✅ Audit report generated with three unchecked checklists
 2. ✅ Each checklist has clear, actionable work items
-3. ✅ Report saved to `trinity/reports/` using Task skill Write
+3. ✅ Report saved to `.claude/trinity/reports/` using Task skill Write
 4. ✅ **Phase 1 complete**
 
 **DO NOT execute any documentation updates.**

package/dist/templates/trinity/templates/documentation/reports/juno-internal-report.md.template

@@ -55,7 +55,7 @@
 **Priority:** {{MVC_PRIORITY}}
 **Estimated Time:** {{MVC_TIME}}
 
-**Template Path:** `trinity/templates/documentation/mermaid-diagrams/mvc-flow.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/mermaid-diagrams/mvc-flow.md.template`
 
 **Variables to Replace:**
 - `{{DATABASE}}`: "{{DATABASE_VALUE}}"
@@ -77,7 +77,7 @@
 **Priority:** {{ER_PRIORITY}}
 **Estimated Time:** {{ER_TIME}}
 
-**Template Path:** `trinity/templates/documentation/mermaid-diagrams/database-er.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/mermaid-diagrams/database-er.md.template`
 
 **Variables to Replace:**
 - `{{DATABASE_TYPE}}`: "{{DATABASE_TYPE_VALUE}}"
@@ -96,7 +96,7 @@
 **Priority:** {{API_MAP_PRIORITY}}
 **Estimated Time:** {{API_MAP_TIME}}
 
-**Template Path:** `trinity/templates/documentation/mermaid-diagrams/api-endpoint-map.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/mermaid-diagrams/api-endpoint-map.md.template`
 
 **Variables to Replace:**
 - `{{BASE_URL}}`: "{{BASE_URL_VALUE}}"
@@ -115,7 +115,7 @@
 **Priority:** {{COMPONENT_PRIORITY}}
 **Estimated Time:** {{COMPONENT_TIME}}
 
-**Template Path:** `trinity/templates/documentation/mermaid-diagrams/component-hierarchy.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/mermaid-diagrams/component-hierarchy.md.template`
 
 **Variables to Replace:**
 - `{{FRAMEWORK}}`: "{{COMPONENT_FRAMEWORK_VALUE}}"
@@ -136,7 +136,7 @@
 **Priority:** {{API_DOCS_PRIORITY}}
 **Estimated Time:** {{API_DOCS_TIME}}
 
-**Template Path:** `trinity/templates/documentation/api-docs/README.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/api-docs/README.md.template`
 
 **Endpoints to Document:** {{ENDPOINT_COUNT}}
 
@@ -174,7 +174,7 @@
 **Priority:** {{GETTING_STARTED_PRIORITY}}
 **Estimated Time:** {{GETTING_STARTED_TIME}}
 
-**Template Path:** `trinity/templates/documentation/guides/getting-started.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/guides/getting-started.md.template`
 
 **Variables to Replace:**
 - `{{PROJECT_NAME}}`: "{{PROJECT_NAME}}"
@@ -207,7 +207,7 @@
 **Priority:** {{API_DEV_PRIORITY}}
 **Estimated Time:** {{API_DEV_TIME}}
 
-**Template Path:** `trinity/templates/documentation/guides/api-development.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/guides/api-development.md.template`
 
 **Variables to Replace:**
 - `{{PROJECT_NAME}}`: "{{PROJECT_NAME}}"
@@ -250,7 +250,7 @@
 **Priority:** {{DEPLOYMENT_PRIORITY}}
 **Estimated Time:** {{DEPLOYMENT_TIME}}
 
-**Template Path:** `trinity/templates/documentation/guides/deployment.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/guides/deployment.md.template`
 
 **Variables to Replace:**
 - `{{PROJECT_NAME}}`: "{{PROJECT_NAME}}"
@@ -297,7 +297,7 @@
 **Priority:** {{CONTRIBUTING_PRIORITY}}
 **Estimated Time:** {{CONTRIBUTING_TIME}}
 
-**Template Path:** `trinity/templates/documentation/guides/contributing.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/guides/contributing.md.template`
 
 **Variables to Replace:**
 - `{{PROJECT_NAME}}`: "{{PROJECT_NAME}}"
@@ -342,7 +342,7 @@
 **Estimated Time:** {{ENV_TIME}}
 
 **Environment Variables Discovered ({{ENV_VAR_COUNT}}):**
-**Template Path:** `trinity/templates/documentation/config/env-example-generator.md.template`
+**Template Path:** `.claude/trinity/templates/documentation/config/env-example-generator.md.template`
 
 **Variables to Replace:**
 - `{{PROJECT_NAME}}`: "{{PROJECT_NAME}}"

package/dist/templates/trinity/templates/investigations/bug.md.template

@@ -399,7 +399,7 @@ describe('Regression: {{title}}', () => {
 
 ### Investigation Report Format
 **Filename:** `INV-{{investigationId}}-findings-[TIMESTAMP].md`
-**Location:** `trinity/reports/`
+**Location:** `.claude/trinity/reports/`
 
 ### Required Sections
 1. **Investigation Summary** - Brief overview of what was investigated
@@ -422,22 +422,22 @@ describe('Regression: {{title}}', () => {
 
 When investigation is complete:
 1. **Create Investigation Report:**
-   - [ ] Save findings report to `trinity/reports/INV-{{investigationId}}-findings-[TIMESTAMP].md`
+   - [ ] Save findings report to `.claude/trinity/reports/INV-{{investigationId}}-findings-[TIMESTAMP].md`
    - [ ] Include all required sections listed above
    - [ ] Attach all evidence and supporting documentation
 
 2. **Move Investigation File:**
-   - [ ] Move this investigation file (INV-{{investigationId}}.md) to `trinity/sessions/`
-   - [ ] Keep report in `trinity/reports/` until end of session
+   - [ ] Move this investigation file (INV-{{investigationId}}.md) to `.claude/trinity/sessions/`
+   - [ ] Keep report in `.claude/trinity/reports/` until end of session
 
 3. **Session Cleanup:**
    - [ ] Run `/trinity-end` to archive both investigation and report
-   - [ ] Investigation will be archived to `trinity/archive/investigations/YYYY-MM-DD/`
-   - [ ] Report will be archived to `trinity/archive/reports/YYYY-MM-DD/`
+   - [ ] Investigation will be archived to `.claude/trinity/archive/investigations/YYYY-MM-DD/`
+   - [ ] Report will be archived to `.claude/trinity/archive/reports/YYYY-MM-DD/`
 
 4. **Clean Slate:**
-   - [ ] Verify `trinity/sessions/` is empty (ready for next session)
-   - [ ] Verify `trinity/reports/` is empty (ready for next session)
+   - [ ] Verify `.claude/trinity/sessions/` is empty (ready for next session)
+   - [ ] Verify `.claude/trinity/reports/` is empty (ready for next session)
 
 ---
 
@@ -445,15 +445,15 @@ When investigation is complete:
 
 **Trinity Method Core:**
 - [Trinity Method Protocols](../../CLAUDE.md) - Root Trinity guidance
-- [Investigation Requirements](../../trinity/CLAUDE.md#investigation-protocols) - Investigation-first methodology
+- [Investigation Requirements](../../.claude/trinity/CLAUDE.md#investigation-protocols) - Investigation-first methodology
 - [Agent Directory](../../.claude/EMPLOYEE-DIRECTORY.md) - 19-agent Trinity team
 
 **Knowledge Base:**
-- [Architecture](../../trinity/knowledge-base/ARCHITECTURE.md) - System architecture and patterns
-- [Known Issues](../../trinity/knowledge-base/ISSUES.md) - Issue patterns database
-- [Technical Debt](../../trinity/knowledge-base/Technical-Debt.md) - Debt tracking
-- [Testing Standards](../../trinity/knowledge-base/TESTING-PRINCIPLES.md) - Test requirements
-- [Coding Standards](../../trinity/knowledge-base/CODING-PRINCIPLES.md) - Code quality
+- [Architecture](../../.claude/trinity/knowledge-base/ARCHITECTURE.md) - System architecture and patterns
+- [Known Issues](../../.claude/trinity/knowledge-base/ISSUES.md) - Issue patterns database
+- [Technical Debt](../../.claude/trinity/knowledge-base/Technical-Debt.md) - Debt tracking
+- [Testing Standards](../../.claude/trinity/knowledge-base/TESTING-PRINCIPLES.md) - Test requirements
+- [Coding Standards](../../.claude/trinity/knowledge-base/CODING-PRINCIPLES.md) - Code quality
 
 **Investigation Protocols:**
 - READ-ONLY: No file modifications during investigation

package/dist/templates/trinity/templates/investigations/feature.md.template

@@ -473,15 +473,15 @@ describe('Feature E2E', () => {
 
 **Trinity Method Core:**
 - [Trinity Method Protocols](../../CLAUDE.md) - Root Trinity guidance
-- [Investigation Requirements](../../trinity/CLAUDE.md#investigation-protocols) - Investigation-first methodology
+- [Investigation Requirements](../../.claude/trinity/CLAUDE.md#investigation-protocols) - Investigation-first methodology
 - [Agent Directory](../../.claude/EMPLOYEE-DIRECTORY.md) - 19-agent Trinity team
 
 **Knowledge Base:**
-- [Architecture](../../trinity/knowledge-base/ARCHITECTURE.md) - System architecture and patterns
-- [Known Issues](../../trinity/knowledge-base/ISSUES.md) - Issue patterns database
-- [Technical Debt](../../trinity/knowledge-base/Technical-Debt.md) - Debt tracking
-- [Testing Standards](../../trinity/knowledge-base/TESTING-PRINCIPLES.md) - Test requirements
-- [Coding Standards](../../trinity/knowledge-base/CODING-PRINCIPLES.md) - Code quality
+- [Architecture](../../.claude/trinity/knowledge-base/ARCHITECTURE.md) - System architecture and patterns
+- [Known Issues](../../.claude/trinity/knowledge-base/ISSUES.md) - Issue patterns database
+- [Technical Debt](../../.claude/trinity/knowledge-base/Technical-Debt.md) - Debt tracking
+- [Testing Standards](../../.claude/trinity/knowledge-base/TESTING-PRINCIPLES.md) - Test requirements
+- [Coding Standards](../../.claude/trinity/knowledge-base/CODING-PRINCIPLES.md) - Code quality
 
 **Investigation Protocols:**
 - READ-ONLY: No file modifications during investigation
@@ -495,7 +495,7 @@ describe('Feature E2E', () => {
 
 ### Investigation Report Format
 **Filename:** `INV-{{investigationId}}-findings-[TIMESTAMP].md`
-**Location:** `trinity/reports/`
+**Location:** `.claude/trinity/reports/`
 
 ### Required Sections
 1. **Investigation Summary** - Feature analysis overview and business value
@@ -519,22 +519,22 @@ describe('Feature E2E', () => {
 
 When investigation is complete:
 1. **Create Investigation Report:**
-   - [ ] Save findings report to `trinity/reports/INV-{{investigationId}}-findings-[TIMESTAMP].md`
+   - [ ] Save findings report to `.claude/trinity/reports/INV-{{investigationId}}-findings-[TIMESTAMP].md`
    - [ ] Include all required sections listed above
    - [ ] Attach all evidence and supporting documentation
 
 2. **Move Investigation File:**
-   - [ ] Move this investigation file (INV-{{investigationId}}.md) to `trinity/sessions/`
-   - [ ] Keep report in `trinity/reports/` until end of session
+   - [ ] Move this investigation file (INV-{{investigationId}}.md) to `.claude/trinity/sessions/`
+   - [ ] Keep report in `.claude/trinity/reports/` until end of session
 
 3. **Session Cleanup:**
    - [ ] Run `/trinity-end` to archive both investigation and report
-   - [ ] Investigation will be archived to `trinity/archive/investigations/YYYY-MM-DD/`
-   - [ ] Report will be archived to `trinity/archive/reports/YYYY-MM-DD/`
+   - [ ] Investigation will be archived to `.claude/trinity/archive/investigations/YYYY-MM-DD/`
+   - [ ] Report will be archived to `.claude/trinity/archive/reports/YYYY-MM-DD/`
 
 4. **Clean Slate:**
-   - [ ] Verify `trinity/sessions/` is empty (ready for next session)
-   - [ ] Verify `trinity/reports/` is empty (ready for next session)
+   - [ ] Verify `.claude/trinity/sessions/` is empty (ready for next session)
+   - [ ] Verify `.claude/trinity/reports/` is empty (ready for next session)
 
 ---
 

package/dist/templates/trinity/templates/investigations/performance.md.template

@@ -537,7 +537,7 @@ describe('Performance: getUserOrders', () => {
 
 ### Investigation Report Format
 **Filename:** `INV-{{investigationId}}-findings-[TIMESTAMP].md`
-**Location:** `trinity/reports/`
+**Location:** `.claude/trinity/reports/`
 
 ### Required Sections
 1. **Investigation Summary** - Performance issue overview and user impact
@@ -561,22 +561,22 @@ describe('Performance: getUserOrders', () => {
 
 When investigation is complete:
 1. **Create Investigation Report:**
-   - [ ] Save findings report to `trinity/reports/INV-{{investigationId}}-findings-[TIMESTAMP].md`
+   - [ ] Save findings report to `.claude/trinity/reports/INV-{{investigationId}}-findings-[TIMESTAMP].md`
    - [ ] Include all required sections listed above
    - [ ] Attach all evidence and supporting documentation
 
 2. **Move Investigation File:**
-   - [ ] Move this investigation file (INV-{{investigationId}}.md) to `trinity/sessions/`
-   - [ ] Keep report in `trinity/reports/` until end of session
+   - [ ] Move this investigation file (INV-{{investigationId}}.md) to `.claude/trinity/sessions/`
+   - [ ] Keep report in `.claude/trinity/reports/` until end of session
 
 3. **Session Cleanup:**
    - [ ] Run `/trinity-end` to archive both investigation and report
-   - [ ] Investigation will be archived to `trinity/archive/investigations/YYYY-MM-DD/`
-   - [ ] Report will be archived to `trinity/archive/reports/YYYY-MM-DD/`
+   - [ ] Investigation will be archived to `.claude/trinity/archive/investigations/YYYY-MM-DD/`
+   - [ ] Report will be archived to `.claude/trinity/archive/reports/YYYY-MM-DD/`
 
 4. **Clean Slate:**
-   - [ ] Verify `trinity/sessions/` is empty (ready for next session)
-   - [ ] Verify `trinity/reports/` is empty (ready for next session)
+   - [ ] Verify `.claude/trinity/sessions/` is empty (ready for next session)
+   - [ ] Verify `.claude/trinity/reports/` is empty (ready for next session)
 
 ---
 
@@ -584,15 +584,15 @@ When investigation is complete:
 
 **Trinity Method Core:**
 - [Trinity Method Protocols](../../CLAUDE.md) - Root Trinity guidance
-- [Investigation Requirements](../../trinity/CLAUDE.md#investigation-protocols) - Investigation-first methodology
+- [Investigation Requirements](../../.claude/trinity/CLAUDE.md#investigation-protocols) - Investigation-first methodology
 - [Agent Directory](../../.claude/EMPLOYEE-DIRECTORY.md) - 19-agent Trinity team
 
 **Knowledge Base:**
-- [Architecture](../../trinity/knowledge-base/ARCHITECTURE.md) - System architecture and patterns
-- [Known Issues](../../trinity/knowledge-base/ISSUES.md) - Issue patterns database
-- [Technical Debt](../../trinity/knowledge-base/Technical-Debt.md) - Debt tracking
-- [Testing Standards](../../trinity/knowledge-base/TESTING-PRINCIPLES.md) - Test requirements
-- [Coding Standards](../../trinity/knowledge-base/CODING-PRINCIPLES.md) - Code quality
+- [Architecture](../../.claude/trinity/knowledge-base/ARCHITECTURE.md) - System architecture and patterns
+- [Known Issues](../../.claude/trinity/knowledge-base/ISSUES.md) - Issue patterns database
+- [Technical Debt](../../.claude/trinity/knowledge-base/Technical-Debt.md) - Debt tracking
+- [Testing Standards](../../.claude/trinity/knowledge-base/TESTING-PRINCIPLES.md) - Test requirements
+- [Coding Standards](../../.claude/trinity/knowledge-base/CODING-PRINCIPLES.md) - Code quality
 
 **Investigation Protocols:**
 - READ-ONLY: No file modifications during investigation