Migration from Docker to Standalone Python Server (#73)

* Migration from docker to standalone server
Migration handling
Fixed tests
Use simpler in-memory storage
Support for concurrent logging to disk
Simplified direct connections to localhost

* Migration from docker / redis to standalone script
Updated tests
Updated run script
Fixed requirements
Use dotenv
Ask if user would like to install MCP in Claude Desktop once
Updated docs

* More cleanup and references to docker removed

* Cleanup

* Comments

* Fixed tests

* Fix GitHub Actions workflow for standalone Python architecture

- Install requirements-dev.txt for pytest and testing dependencies
- Remove Docker setup from simulation tests (now standalone)
- Simplify linting job to use requirements-dev.txt
- Update simulation tests to run directly without Docker

Fixes unit test failures in CI due to missing pytest dependency.

🤖 Generated with [Claude Code](https://claude.ai/code)

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

* Remove simulation tests from GitHub Actions

- Removed simulation-tests job that makes real API calls
- Keep only unit tests (mocked, no API costs) and linting
- Simulation tests should be run manually with real API keys
- Reduces CI costs and complexity

GitHub Actions now only runs:
- Unit tests (569 tests, all mocked)
- Code quality checks (ruff, black)

🤖 Generated with [Claude Code](https://claude.ai/code)

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

* Fixed tests

* Fixed tests

---------

Co-authored-by: Claude <noreply@anthropic.com>

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -11,8 +11,8 @@ body:
     id: version
     attributes:
       label: Project Version
-      description: "Which version are you using? (e.g., Docker image tag like `latest` or `v1.2.3`, or a git commit SHA)"
-      placeholder: "e.g., ghcr.io/beehiveinnovations/zen-mcp-server:latest"
+      description: "Which version are you using? (To see version: ./run-server.sh -v)"
+      placeholder: "e.g., 5.1.0"
     validations:
       required: true
 
@@ -29,7 +29,7 @@ body:
     id: logs
     attributes:
       label: Relevant Log Output
-      description: "Please copy and paste any relevant log output. You can obtain these from the MCP folder by running `docker compose logs`."
+      description: "Please copy and paste any relevant log output. Logs are stored under the `logs` folder in the zen folder. You an also use `./run-server.sh -f` to see logs"
       render: shell
 
   - type: dropdown

.github/ISSUE_TEMPLATE/documentation.yml

@@ -33,7 +33,7 @@ body:
     attributes:
       label: What is wrong with the documentation?
       description: "Please describe the problem. Be specific about what is unclear, incorrect, or missing."
-      placeholder: "The Docker setup command in the README is missing the `--pull=always` flag, which means users might use an outdated image version."
+      placeholder: "README is missing some details"
     validations:
       required: true
 
@@ -42,16 +42,8 @@ body:
     attributes:
       label: Suggested Improvement
       description: "How can we make it better? If you can, please provide the exact text or changes you'd like to see."
-      placeholder: |
-        Change:
-        ```
-        docker run ghcr.io/beehiveinnovations/zen-mcp-server:latest
-        ```
-        
-        To:
-        ```
-        docker run --pull=always ghcr.io/beehiveinnovations/zen-mcp-server:latest
-        ```
+      placeholder: "Please improve...."
+
 
   - type: dropdown
     id: audience

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -33,7 +33,7 @@ body:
       label: Feature Category
       description: What type of enhancement is this?
       options:
-        - New Gemini tool (chat, codereview, debug, etc.)
+        - New tool (chat, codereview, debug, etc.)
         - Workflow improvement
         - Integration enhancement
         - Performance optimization

.github/ISSUE_TEMPLATE/tool_addition.yml

@@ -1,12 +1,12 @@
 name: 🛠️ New Gemini Tool Proposal
-description: Propose a new Gemini MCP tool (e.g., `summarize`, `testgen`, `refactor`)
+description: Propose a new Zen MCP tool (e.g., `summarize`, `fixer`, `refactor`)
 labels: ["enhancement", "new-tool"]
 body:
   - type: input
     id: tool-name
     attributes:
       label: Proposed Tool Name
-      description: "What would the tool be called? (e.g., `summarize`, `testgen`, `refactor`)"
+      description: "What would the tool be called? (e.g., `summarize`, `docgen`, `refactor`)"
       placeholder: "e.g., `docgen`"
     validations:
       required: true
@@ -15,7 +15,7 @@ body:
     id: purpose
     attributes:
       label: What is the primary purpose of this tool?
-      description: "Explain the tool's core function and the value it provides to developers using Claude + Gemini."
+      description: "Explain the tool's core function and the value it provides to developers using Claude + Zen."
       placeholder: "This tool will automatically generate comprehensive documentation from code, extracting class and function signatures, docstrings, and creating usage examples."
     validations:
       required: true
@@ -27,9 +27,9 @@ body:
       description: "Show how a user would invoke this tool through Claude and what the expected output would look like."
       placeholder: |
         **User prompt to Claude:**
-        "Use gemini to generate documentation for my entire src/ directory"
+        "Use zen to generate documentation for my entire src/ directory"
 
-        **Expected Gemini tool behavior:**
+        **Expected behavior:**
         - Analyze all Python files in src/
         - Extract classes, functions, and their docstrings
         - Generate structured markdown documentation
@@ -61,7 +61,7 @@ body:
     id: system-prompt
     attributes:
       label: Proposed System Prompt (Optional)
-      description: "If you have ideas for how Gemini should be prompted for this tool, share them here."
+      description: "If you have ideas for how zen should be prompted for this tool, share them here."
       placeholder: |
         You are an expert technical documentation generator. Your task is to create comprehensive, user-friendly documentation from source code...