feat: add configurable environment variable override system

Add ZEN_MCP_FORCE_ENV_OVERRIDE configuration to control whether .env file values
override system environment variables. This prevents conflicts when multiple AI
tools pass different cached environment variables to the MCP server.

- Use dotenv_values() to read configuration from .env file only
- Apply conditional override based on configuration setting
- Add appropriate logging for transparency
- Update .env.example with detailed configuration documentation
- Maintains backward compatibility with default behavior (false)

.env.example

@@ -167,6 +167,31 @@ DISABLED_TOOLS=analyze,refactor,testgen,secaudit,docgen,tracer
 # Leave empty for default language (English)
 # LOCALE=fr-FR
 
+# ===========================================
+# Zen MCP Server Configuration  
+# ===========================================
+
+# Force .env file values to override system environment variables
+# This prevents issues where different AI tools (Claude Code, etc.) pass 
+# conflicting or cached environment variables that override each other
+# 
+# When enabled (true):
+#   - .env file values take absolute precedence
+#   - Prevents MCP clients from passing outdated/cached API keys
+#   - Ensures consistent configuration across different AI tool integrations
+#   - Solves environment variable conflicts between multiple AI applications
+#
+# When disabled (false):
+#   - System environment variables take precedence (standard behavior)  
+#   - Suitable for production deployments with secure environment injection
+#   - Respects container orchestrator and CI/CD pipeline configurations
+#
+# Recommended settings:
+#   Development with multiple AI tools: true (prevents tool conflicts)
+#   Production/Container deployments: false (preserves security practices)
+#   CI/CD environments: false (respects pipeline secrets)
+ZEN_MCP_FORCE_ENV_OVERRIDE=false
+
 # ===========================================
 # Docker Configuration
 # ===========================================