Document PM2R_HOME and multi-instance support

Adds documentation for the `PM2R_HOME` environment variable,
allowing users to specify a custom configuration directory.

Also documents better support for running multiple isolated PMDaemon instances.
This allows for running multiple instances without conflicts,
improving isolation and reliability.

Corrects links in the documentation.

Author: entrepeneur4lyf

docs/changelog/2025-05-27-v0.1.2.md

@@ -26,6 +26,8 @@ This release represents two major milestones: **ecosystem configuration support*
 - **Comprehensive Field Support** - All process options configurable via files
 - **Environment-Specific Configs** - Separate config files for different environments
 - **Validation & Error Handling** - Detailed error messages for configuration issues
+- **Custom Configuration Directory** - `PM2R_HOME` environment variable support for configuration directory override
+- **Multi-Instance Support** - Better support for running multiple isolated PMDaemon instances
 
 ### 🌍 Cross-Platform Support
 - **Native Windows Support** - Full functionality on Windows 10/11 with optimized process management
@@ -65,6 +67,19 @@ pmdaemon --config ecosystem.json start
 pmdaemon --config ecosystem.json start --name web-server
 ```
 
+### Environment Variable Configuration
+
+**Custom Configuration Directory:**
+```bash
+# Use custom config directory
+export PM2R_HOME="/path/to/custom/config"
+pmdaemon start "node server.js" --name web-app
+
+# Multiple isolated instances
+PM2R_HOME="/tmp/instance1" pmdaemon start app1.js --name app1
+PM2R_HOME="/tmp/instance2" pmdaemon start app2.js --name app2
+```
+
 ### Cross-Platform Installation
 
 **Pre-built Binaries:**
@@ -102,6 +117,8 @@ PMDaemon v0.1.2 now matches and exceeds PM2's capabilities across all platforms:
 | Auto port assignment   | ✅              | ❌  |
 | Built-in health checks | ✅              | ❌  |
 | Configuration validation| ✅              | ❌  |
+| Custom config directory | ✅ (PM2R_HOME)  | ❌  |
+| Multi-instance isolation| ✅              | ❌  |
 
 ## 📚 Migration from PM2
 
@@ -133,8 +150,8 @@ module.exports = {
 ## 🔗 Resources
 
 - **[Configuration Guide](/docs/configuration/ecosystem-files)** - Complete ecosystem config documentation
-- **[Examples](/docs/examples/use-cases)** - Real-world configuration examples
-- **[Migration Guide](/docs/getting-started/migration-from-pm2)** - Step-by-step PM2 migration
+- **[Examples](/docs/examples/ecosystem-configs)** - Real-world configuration examples
+- **[Migration Guide](/docs/comparison/migration-from-pm2)** - Step-by-step PM2 migration
 
 ---