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