feat(env): update .env.example with new tool configurations and rate limiting settings

Signed-off-by: Adam Shedivy <ajshedivyaj@gmail.com>

Author: ajshedivy

.env.example

@@ -40,7 +40,7 @@ DB2i_IGNORE_UNAUTHORIZED=true
 #   - Directory: tools/ (loads all .yaml/.yml files)
 #   - Glob: tools/**/*.yaml
 # Default: none (no tools loaded)
-TOOLS_YAML_PATH=tools
+TOOLS_YAML_PATH=
 
 # Comma-separated list of toolsets to load (filters available tools)
 # Leave empty to load all tools
@@ -74,9 +74,17 @@ YAML_VALIDATE_MERGED=true
 # 🛠️ Built-in Tools Configuration
 # -----------------------------------------------------------------------------
 
-# Enable the built-in execute_sql tool for ad-hoc SELECT queries
+# Enable the default text-to-SQL toolset (list_schemas, list_tables_in_schema,
+# get_table_columns, get_related_objects, validate_query)
 # Default: false
-# ⚠️ SECURITY: This tool allows clients to run arbitrary SELECT queries.
+# CLI equivalent: --builtin-tools
+# These are read-only schema discovery tools that query IBM i catalog views.
+IBMI_ENABLE_DEFAULT_TOOLS=false
+
+# Enable the built-in execute_sql tool for ad-hoc SQL queries
+# Default: false
+# CLI equivalent: --execute-sql
+# ⚠️ SECURITY: This tool allows clients to run arbitrary SQL queries.
 #              Enable only in development or trusted environments.
 #              Consider using YAML-defined tools in production for better control.
 # See: https://github.com/IBM/ibmi-mcp-server#built-in-tools-configuration
@@ -159,6 +167,45 @@ MCP_HTTP_PORT_RETRY_DELAY_MS=50
 # Example: http://localhost:3000,https://app.example.com
 MCP_ALLOWED_ORIGINS=
 
+# -----------------------------------------------------------------------------
+# 🛡️ Rate Limiting (HTTP Only)
+# -----------------------------------------------------------------------------
+# Controls request rate limiting for the HTTP transport.
+# Disable or increase limits for agentic workflows with parallel tool calls.
+
+# Enable or disable rate limiting
+# Default: true
+MCP_RATE_LIMIT_ENABLED=true
+
+# Maximum requests allowed per window
+# Default: 100
+# Tip: Increase for AI agent workflows that make many parallel tool calls
+MCP_RATE_LIMIT_MAX_REQUESTS=100
+
+# Rate limit window duration in milliseconds
+# Default: 900000 (15 minutes)
+MCP_RATE_LIMIT_WINDOW_MS=900000
+
+# Skip rate limiting in development (NODE_ENV=development)
+# Default: false
+MCP_RATE_LIMIT_SKIP_DEV=false
+
+# -----------------------------------------------------------------------------
+# 🔄 Connection Pool Timeouts
+# -----------------------------------------------------------------------------
+# Controls automatic cleanup of idle Mapepire connection pools and query timeouts.
+# Essential for cloud deployments (Railway, Heroku, etc.) where proxies kill idle connections.
+
+# Idle timeout for Mapepire connection pools (ms). Pools closed after inactivity.
+# Fresh connections established automatically on next request.
+# Set to 0 to disable. Default: 300000 (5 minutes)
+MCP_POOL_IDLE_TIMEOUT_MS=300000
+
+# Query execution timeout (ms). Queries aborted after this period.
+# Pool re-initialized on next request after timeout.
+# Set to 0 to disable. Default: 30000 (30 seconds)
+MCP_POOL_QUERY_TIMEOUT_MS=30000
+
 # -----------------------------------------------------------------------------
 # 🔐 Authentication & Authorization
 # -----------------------------------------------------------------------------