fix: resolve pixi environment configuration warnings

.claude/state/ci_complete_fix.json

@@ -0,0 +1,114 @@
+{
+  "session_id": "ci-fix-cycle4-integration-issues-20250725",
+  "restart_count": 3,
+  "max_restarts": 3,
+  "total_tests": 8,
+  "failing_tests": [
+    {
+      "job_name": "test-matrix (3.12, integration)",
+      "test_name": "test_add_and_search_pattern",
+      "error_type": "assert False",
+      "file_path": "tests/integration/test_knowledge_manager_integration.py",
+      "line": 87,
+      "status": "NEW_PATTERN",
+      "fix_attempt": 0,
+      "fix_description": "Database operations failing with assert False instead of None",
+      "root_cause": "Integration test logic changed - no longer testing for None but getting False results"
+    },
+    {
+      "job_name": "test-matrix (3.12, integration)",
+      "test_name": "test_add_and_search_error_solution",
+      "error_type": "assert False",
+      "file_path": "tests/integration/test_knowledge_manager_integration.py",
+      "line": 141,
+      "status": "NEW_PATTERN",
+      "fix_attempt": 0,
+      "fix_description": "Error solution operations failing with assert False"
+    },
+    {
+      "job_name": "test-and-coverage",
+      "test_name": "test_update_and_delete_pattern",
+      "error_type": "assert False",
+      "file_path": "tests/integration/test_knowledge_manager_integration.py",
+      "line": 167,
+      "status": "NEW_PATTERN",
+      "fix_attempt": 0,
+      "fix_description": "Pattern update/delete operations failing"
+    },
+    {
+      "job_name": "test-and-coverage",
+      "test_name": "TestEnhancedSemanticSearchEngine.test_engine_initialization_success",
+      "error_type": "AttributeError: module 'uckn.core' has no attribute 'enhanced_semantic_search_engine'",
+      "file_path": "tests/unit/atoms/test_semantic_search_engine.py",
+      "line": 1393,
+      "status": "IMPORT_ERROR",
+      "fix_attempt": 0,
+      "fix_description": "Missing module attribute after refactoring"
+    },
+    {
+      "job_name": "PR Quality Gate",
+      "test_name": "GitHub Actions Cache Service",
+      "error_type": "Cache service responded with 400",
+      "file_path": ".github/workflows/pr-checks.yml",
+      "line": 10,
+      "status": "INFRASTRUCTURE",
+      "fix_attempt": 0,
+      "fix_description": "GitHub infrastructure issue - cache service unavailable"
+    },
+    {
+      "job_name": "All test jobs",
+      "test_name": "Pydantic WorkflowState serialization",
+      "error_type": "PydanticSerializationUnexpectedValue",
+      "file_path": ".pixi/envs/quality/lib/python3.12/site-packages/pydantic/main.py",
+      "line": 463,
+      "status": "WARNING",
+      "fix_attempt": 0,
+      "fix_description": "Enum serialization warnings - not blocking but should be fixed"
+    },
+    {
+      "job_name": "test-matrix (3.12, unit)",
+      "test_name": "test_add_and_search_pattern",
+      "error_type": "assert False",
+      "file_path": "tests/integration/test_knowledge_manager_integration.py",
+      "line": 87,
+      "status": "DUPLICATE",
+      "fix_attempt": 0,
+      "fix_description": "Same test failing in unit test matrix"
+    },
+    {
+      "job_name": "test-matrix (3.12, e2e)",
+      "test_name": "test_add_and_search_pattern",
+      "error_type": "assert False",
+      "file_path": "tests/integration/test_knowledge_manager_integration.py",
+      "line": 87,
+      "status": "DUPLICATE",
+      "fix_attempt": 0,
+      "fix_description": "Same test failing in e2e test matrix"
+    }
+  ],
+  "current_test_index": 0,
+  "completed_tests": [
+    {
+      "test_name": "pixi install infrastructure",
+      "job_name": "All CI jobs",
+      "attempts_needed": 3,
+      "fixed_at": "2025-07-24T15:30:00Z",
+      "status": "MAJOR_BREAKTHROUGH"
+    }
+  ],
+  "failed_to_fix": [],
+  "started_at": "2025-07-25T18:53:00Z",
+  "status": "pattern_evolution_detected",
+  "total_iterations_used": 16,
+  "pattern_evolution": {
+    "previous_pattern": "assert None is not None - database operations returning None",
+    "current_pattern": "assert False - generic assertion failures in integration tests",
+    "evolution_cause": "Pixi fix revealed underlying test logic issues masked by infrastructure problems",
+    "priority_order": [
+      "IMPORT_ERROR - missing module attributes (blocking)",
+      "NEW_PATTERN - integration test assertion failures (critical)",
+      "WARNING - Pydantic serialization warnings (medium)",
+      "INFRASTRUCTURE - GitHub cache service (external)"
+    ]
+  }
+}

.env.example

@@ -7,4 +7,4 @@ MISTRAL_API_KEY="your_mistral_key_here"               # Optional, for Mistral AI
 XAI_API_KEY="YOUR_XAI_KEY_HERE"                       # Optional, for xAI AI models.
 AZURE_OPENAI_API_KEY="your_azure_key_here"            # Optional, for Azure OpenAI models (requires endpoint in .taskmaster/config.json).
 OLLAMA_API_KEY="your_ollama_api_key_here"             # Optional: For remote Ollama servers that require authentication.
-GITHUB_API_KEY="your_github_api_key_here"             # Optional: For GitHub import/export features. Format: ghp_... or github_pat_...
+GITHUB_API_KEY="your_github_api_key_here"             # Optional: For GitHub import/export features. Format: ghp_... or github_pat_...

.github/ISSUE_TEMPLATE/bug_report.md

@@ -38,4 +38,4 @@ Paste any relevant error messages or logs here
 Add any other context about the problem here.
 
 **Knowledge patterns affected**
-If this bug affects knowledge pattern search or recommendations, please describe which patterns are involved.
+If this bug affects knowledge pattern search or recommendations, please describe which patterns are involved.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -30,4 +30,4 @@ Add any other context or screenshots about the feature request here.
 **Integration requirements**
 - Claude Code integration: [yes/no and details]
 - MCP server requirements: [any specific needs]
-- Third-party tools: [GitHub, GitLab, CI/CD systems, etc.]
+- Third-party tools: [GitHub, GitLab, CI/CD systems, etc.]

.github/ISSUE_TEMPLATE/knowledge_pattern.md

@@ -60,4 +60,4 @@ How do you know this pattern works? What are the success indicators?
 - Success rate: [if known, e.g. 95% successful applications]
 
 **Related patterns**
-List any related or prerequisite patterns in UCKN.
+List any related or prerequisite patterns in UCKN.

.github/instructions/dev_workflow.md

@@ -33,7 +33,7 @@ All your standard command executions should operate on the user's current task c
 For new projects or when users are getting started, operate within the `master` tag context:
 
 -   Start new projects by running `initialize_project` tool / `task-master init` or `parse_prd` / `task-master parse-prd --input='<prd-file.txt>'` (see @`taskmaster.md`) to generate initial tasks.json with tagged structure
--   Configure rule sets during initialization with `--rules` flag (e.g., `task-master init --rules vscode,windsurf`) or manage them later with `task-master rules add/remove` commands  
+-   Configure rule sets during initialization with `--rules` flag (e.g., `task-master init --rules vscode,windsurf`) or manage them later with `task-master rules add/remove` commands
 -   Begin coding sessions with `get_tasks` / `task-master list` (see @`taskmaster.md`) to see current tasks, status, and IDs
 -   Determine the next task to work on using `next_task` / `task-master next` (see @`taskmaster.md`)
 -   Analyze task complexity with `analyze_project_complexity` / `task-master analyze-complexity --research` (see @`taskmaster.md`) before breaking down tasks
@@ -136,7 +136,7 @@ Once you transition to tag-based workflows, the `master` tag should ideally cont
 1. **Identify the Initiative**: When user describes a significant feature
 2. **Create Dedicated Tag**: `add_tag feature-[name] --description="[Feature description]"`
 3. **Collaborative PRD Creation**: Work with user to create comprehensive PRD in `.taskmaster/docs/feature-[name]-prd.txt`
-4. **Parse & Prepare**: 
+4. **Parse & Prepare**:
    - `parse_prd .taskmaster/docs/feature-[name]-prd.txt --tag=feature-[name]`
    - `analyze_project_complexity --tag=feature-[name] --research`
    - `expand_all --tag=feature-[name] --research`
@@ -168,7 +168,7 @@ Action: add_tag my-api-work --copy-from-current --description="My API tasks whil
 ```
 User: "I want to add a complete user dashboard with analytics, user management, and reporting"
 Your Response: "This sounds like a major feature that would benefit from detailed planning. Let me create a dedicated context for this work and we can draft a PRD together to ensure we capture all requirements."
-Actions: 
+Actions:
 1. add_tag feature-dashboard --description="User dashboard with analytics and management"
 2. Collaborate on PRD creation
 3. parse_prd dashboard-prd.txt --tag=feature-dashboard
@@ -263,9 +263,9 @@ Taskmaster offers two primary ways to interact:
     - Dependencies are displayed with status indicators (✅ for completed, ⏱️ for pending)
     - This helps quickly identify which prerequisite tasks are blocking work
 - **priority**: Importance level (Example: `"high"`, `"medium"`, `"low"`)
-- **details**: In-depth implementation instructions (Example: `"Use GitHub client ID/secret, handle callback, set session token."`) 
-- **testStrategy**: Verification approach (Example: `"Deploy and call endpoint to confirm 'Hello World' response."`) 
-- **subtasks**: List of smaller, more specific tasks (Example: `[{"id": 1, "title": "Configure OAuth", ...}]`) 
+- **details**: In-depth implementation instructions (Example: `"Use GitHub client ID/secret, handle callback, set session token."`)
+- **testStrategy**: Verification approach (Example: `"Deploy and call endpoint to confirm 'Hello World' response."`)
+- **subtasks**: List of smaller, more specific tasks (Example: `[{"id": 1, "title": "Configure OAuth", ...}]`)
 - Refer to task structure details (previously linked to `tasks.md`).
 
 ## Configuration Management (Updated)
@@ -345,7 +345,7 @@ Taskmaster supports multiple AI coding assistant rule sets that can be configure
 - Use `move_task` / `task-master move --from=<id> --to=<id>` to move tasks or subtasks within the hierarchy
 - This command supports several use cases:
   - Moving a standalone task to become a subtask (e.g., `--from=5 --to=7`)
-  - Moving a subtask to become a standalone task (e.g., `--from=5.2 --to=7`) 
+  - Moving a subtask to become a standalone task (e.g., `--from=5.2 --to=7`)
   - Moving a subtask to a different parent (e.g., `--from=5.2 --to=7.3`)
   - Reordering subtasks within the same parent (e.g., `--from=5.2 --to=5.4`)
   - Moving a task to a new, non-existent ID position (e.g., `--from=5 --to=25`)
@@ -421,4 +421,4 @@ Once a task has been broken down into subtasks using `expand_task` or similar me
     - Can help compare functions between files during migrations or identify potential naming conflicts.
 
 ---
-*This workflow provides a general guideline. Adapt it based on your specific project needs and team practices.*
+*This workflow provides a general guideline. Adapt it based on your specific project needs and team practices.*

.github/instructions/self_improve.md

@@ -38,7 +38,7 @@ alwaysApply: true
     select: { id: true, email: true },
     where: { status: 'ACTIVE' }
   });
-  
+
   // Consider adding to [prisma.md](.github/instructions/prisma.md):
   // - Standard select fields
   // - Common where conditions

.github/instructions/taskmaster.md

@@ -8,7 +8,7 @@ alwaysApply: true
 
 This document provides a detailed reference for interacting with Taskmaster, covering both the recommended MCP tools, suitable for integrations like VS Code, and the corresponding `task-master` CLI commands, designed for direct user interaction or fallback.
 
-**Note:** For interacting with Taskmaster programmatically or via integrated tools, using the **MCP tools is strongly recommended** due to better performance, structured data, and error handling. The CLI commands serve as a user-friendly alternative and fallback. 
+**Note:** For interacting with Taskmaster programmatically or via integrated tools, using the **MCP tools is strongly recommended** due to better performance, structured data, and error handling. The CLI commands serve as a user-friendly alternative and fallback.
 
 **Important:** Several MCP tools involve AI processing... The AI-powered tools include `parse_prd`, `analyze_project_complexity`, `update_subtask`, `update_task`, `update`, `expand_all`, `expand_task`, and `add_task`.
 
@@ -38,8 +38,8 @@ This document provides a detailed reference for interacting with Taskmaster, cov
     *   `skipInstall`: `Skip installing dependencies. Default is false.` (CLI: `--skip-install`)
     *   `addAliases`: `Add shell aliases tm and taskmaster. Default is false.` (CLI: `--aliases`)
     *   `yes`: `Skip prompts and use defaults/provided arguments. Default is false.` (CLI: `-y, --yes`)
-*   **Usage:** Run this once at the beginning of a new project, typically via an integrated tool like VS Code. Operates on the current working directory of the MCP server. 
-*   **Important:** Once complete, you *MUST* parse a prd in order to generate tasks. There will be no tasks files until then. The next step after initializing should be to create a PRD using the example PRD in .taskmaster/templates/example_prd.txt. 
+*   **Usage:** Run this once at the beginning of a new project, typically via an integrated tool like VS Code. Operates on the current working directory of the MCP server.
+*   **Important:** Once complete, you *MUST* parse a prd in order to generate tasks. There will be no tasks files until then. The next step after initializing should be to create a PRD using the example PRD in .taskmaster/templates/example_prd.txt.
 *   **Tagging:** Use the `--tag` option to parse the PRD into a specific, non-default tag context. If the tag doesn't exist, it will be created automatically. Example: `task-master parse-prd spec.txt --tag=new-feature`.
 
 ### 2. Parse PRD (`parse_prd`)
@@ -84,7 +84,7 @@ This document provides a detailed reference for interacting with Taskmaster, cov
 *   **Usage (CLI):** Run without flags to view current configuration and available models. Use set flags to update specific roles. Use `--setup` for guided configuration, including custom models. To set a custom model via flags, use `--set-<role>=<model_id>` along with either `--ollama` or `--openrouter`.
 *   **Notes:** Configuration is stored in `.taskmaster/config.json` in the project root. This command/tool modifies that file. Use `listAvailableModels` or `task-master models` to see internally supported models. OpenRouter custom models are validated against their live API. Ollama custom models are not validated live.
 *   **API note:** API keys for selected AI providers (based on their model) need to exist in the mcp.json file to be accessible in MCP context. The API keys must be present in the local .env file for the CLI to be able to read them.
-*   **Model costs:** The costs in supported models are expressed in dollars. An input/output value of 3 is $3.00. A value of 0.8 is $0.80. 
+*   **Model costs:** The costs in supported models are expressed in dollars. An input/output value of 3 is $3.00. A value of 0.8 is $0.80.
 *   **Warning:** DO NOT MANUALLY EDIT THE .taskmaster/config.json FILE. Use the included commands either in the MCP or CLI format as needed. Always prioritize MCP tools when available and use the CLI as a fallback.
 
 ---
@@ -555,4 +555,4 @@ Environment variables are used **only** for sensitive API keys related to AI pro
 
 ---
 
-For details on how these commands fit into the development process, see the [dev_workflow.md](.github/instructions/dev_workflow.md).
+For details on how these commands fit into the development process, see the [dev_workflow.md](.github/instructions/dev_workflow.md).

.github/instructions/vscode_rules.md

@@ -27,7 +27,7 @@ alwaysApply: true
   ```typescript
   // ✅ DO: Show good examples
   const goodExample = true;
-  
+
   // ❌ DON'T: Show anti-patterns
   const badExample = false;
   ```
@@ -50,4 +50,4 @@ alwaysApply: true
   - Keep descriptions concise
   - Include both DO and DON'T examples
   - Reference actual code over theoretical examples
-  - Use consistent formatting across rules 
+  - Use consistent formatting across rules

.github/pull_request_template.md

@@ -59,4 +59,4 @@ Any additional information or context for reviewers.
 - Test CLI commands if modified
 - Validate knowledge patterns for accuracy
 - Check TaskMaster integration if applicable
-- Ensure documentation is updated
+- Ensure documentation is updated

.github/workflows/README.md

@@ -6,7 +6,7 @@ This directory contains comprehensive GitHub Actions workflows for automated tes
 
 ### Core CI/CD Pipeline (`ci.yml`)
 - **Triggers**: Push/PR to main/development branches, releases
-- **Jobs**: 
+- **Jobs**:
   - Cross-platform testing (Ubuntu, macOS, Windows)
   - Multi-Python version support (3.10, 3.11, 3.12)
   - Code quality checks (lint, format, type checking)
@@ -74,7 +74,7 @@ The framework uses pytest markers for organized test execution:
 def test_component_functionality():
     """Isolated component testing"""
 
-# Integration Tests  
+# Integration Tests
 @pytest.mark.integration
 def test_component_interactions():
     """Component interaction testing"""
@@ -195,7 +195,7 @@ PIXI_ENV: ci
 ```yaml
 GITHUB_TOKEN: # Automatic
 SMTP_USERNAME: # Email notifications
-SMTP_PASSWORD: # Email notifications  
+SMTP_PASSWORD: # Email notifications
 NOTIFY_EMAILS: # Email recipients
 ```
 
@@ -207,16 +207,16 @@ graph TD
     A --> C[lint]
     A --> D[security]
     A --> E[atomic-design-validation]
-    
+
     F[comprehensive-testing.yml] --> G[changed-files]
     F --> H[test execution]
-    
+
     I[test-matrix.yml] --> J[matrix tests]
     I --> K[aggregate results]
-    
+
     L[performance-testing.yml] --> M[benchmarks]
     L --> N[load tests]
-    
+
     O[quality-metrics.yml] --> P[coverage analysis]
     O --> Q[quality gates]
 ```
@@ -282,4 +282,4 @@ pixi run load-test              # Interactive load testing
 3. Configure reporting formats
 4. Integrate external tools
 
-This comprehensive testing infrastructure ensures high-quality, reliable, and performant code delivery for the UCKN framework.
+This comprehensive testing infrastructure ensures high-quality, reliable, and performant code delivery for the UCKN framework.