env cleanup round 2

DEPRECATED_FILES.md

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+# Deprecated Files - Safe to Delete
+
+This file lists all deprecated files that can be safely deleted after verification.
+
+## Files Marked for Deletion
+
+### Docker Compose Files
+
+#### `/core/docker-compose.yml.DEPRECATED`
+- **Status**: DEPRECATED
+- **Reason**: All services consolidated into main `/docker-compose.yml`
+- **Replaced by**: `/docker-compose.yml` (relay service now has complete config)
+- **Safe to delete**: Yes, after verifying main docker-compose works
+
+### Environment Files
+
+All original `.env` files have been consolidated. Backups exist in `.env-backups/` directory.
+
+#### Previously Deleted (Already Done)
+- ✅ `/core/.env` - Deleted (redundant with root .env)
+
+### Experimental/Orphaned Files
+
+#### `/core/env experiments/` (entire directory)
+- **Status**: User will handle separately
+- **Contains**: `.env`, `.env.local`, `.env.openai`
+- **Action**: User to review and clean up
+
+## Verification Steps Before Deleting
+
+Before deleting the deprecated files, verify:
+
+1. **Test main docker-compose.yml works:**
+   ```bash
+   cd /home/serversdown/project-lyra
+   docker-compose down
+   docker-compose up -d
+   docker-compose ps  # All services should be running
+   ```
+
+2. **Verify relay service has correct config:**
+   ```bash
+   docker exec relay env | grep -E "LLM_|NEOMEM_|OPENAI"
+   docker exec relay ls -la /app/sessions  # Sessions volume mounted
+   ```
+
+3. **Test relay functionality:**
+   - Send a test message through relay
+   - Verify memory storage works
+   - Confirm LLM backend connections work
+
+## Deletion Commands
+
+After successful verification, run:
+
+```bash
+cd /home/serversdown/project-lyra
+
+# Delete deprecated docker-compose file
+rm core/docker-compose.yml.DEPRECATED
+
+# Optionally clean up backup directory after confirming everything works
+# (Keep backups for at least a few days/weeks)
+# rm -rf .env-backups/
+```
+
+## Files to Keep
+
+These files should **NOT** be deleted:
+
+- ✅ `.env` (root) - Single source of truth
+- ✅ `.env.example` (root) - Security template (commit to git)
+- ✅ `cortex/.env` - Service-specific config
+- ✅ `cortex/.env.example` - Security template (commit to git)
+- ✅ `neomem/.env` - Service-specific config
+- ✅ `neomem/.env.example` - Security template (commit to git)
+- ✅ `intake/.env` - Service-specific config
+- ✅ `intake/.env.example` - Security template (commit to git)
+- ✅ `rag/.env.example` - Security template (commit to git)
+- ✅ `docker-compose.yml` - Main orchestration file
+- ✅ `ENVIRONMENT_VARIABLES.md` - Documentation
+- ✅ `.gitignore` - Git configuration
+
+## Backup Information
+
+All original `.env` files backed up to:
+- Location: `/home/serversdown/project-lyra/.env-backups/`
+- Timestamp: `20251126_025334`
+- Files: 6 original .env files
+
+Keep backups until you're confident the new setup is stable (recommended: 2-4 weeks).